PDB Short entry for 6NKU
HEADER    TRANSCRIPTION/DNA                       07-JAN-19   6NKU              
TITLE     TERNARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH "HOT-   
TITLE    2 SPOT SEQUENCE" WITH DGTP                                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-
COMPND   3 3');                                                                 
COMPND   4 CHAIN: T;                                                            
COMPND   5 EC: 2.7.7.7;                                                         
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MOL_ID: 2;                                                           
COMPND   8 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3');          
COMPND   9 CHAIN: P;                                                            
COMPND  10 ENGINEERED: YES;                                                     
COMPND  11 MOL_ID: 3;                                                           
COMPND  12 MOLECULE: DNA (5'-D(P*TP*TP*CP*GP*G)-3');                            
COMPND  13 CHAIN: D;                                                            
COMPND  14 ENGINEERED: YES;                                                     
COMPND  15 MOL_ID: 4;                                                           
COMPND  16 MOLECULE: DNA POLYMERASE BETA;                                       
COMPND  17 CHAIN: A;                                                            
COMPND  18 EC: 2.7.7.7,4.2.99.-;                                                
COMPND  19 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 MOL_ID: 2;                                                           
SOURCE   6 SYNTHETIC: YES;                                                      
SOURCE   7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   8 ORGANISM_TAXID: 9606;                                                
SOURCE   9 MOL_ID: 3;                                                           
SOURCE  10 SYNTHETIC: YES;                                                      
SOURCE  11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  12 ORGANISM_TAXID: 9606;                                                
SOURCE  13 MOL_ID: 4;                                                           
SOURCE  14 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  15 ORGANISM_COMMON: HUMAN;                                              
SOURCE  16 ORGANISM_TAXID: 9606;                                                
SOURCE  17 GENE: POLB;                                                          
SOURCE  18 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE  19 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE  20 EXPRESSION_SYSTEM_VARIANT: TAP56;                                    
SOURCE  21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  22 EXPRESSION_SYSTEM_PLASMID: PWL11                                     
KEYWDS    DNA POLYMERASE BETA, CONFORMATIONAL CHANGE, ENZYME MECHANISM,         
KEYWDS   2 TRANSCRIPTION-DNA COMPLEX                                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    V.K.BATRA,S.H.WILSON                                                  
REVDAT   2   22-JUL-20 6NKU    1       JRNL                                     
REVDAT   1   08-JAN-20 6NKU    0                                                
JRNL        AUTH   V.K.BATRA,K.S.ALNAJJAR,J.B.SWEASY,C.E.MCKENNA,M.F.GOODMAN,   
JRNL        AUTH 2 S.H.WILSON                                                   
JRNL        TITL   REVEALING AN INTERNAL STABILIZATION DEFICIENCY IN THE DNA    
JRNL        TITL 2 POLYMERASE BETA K289M CANCER VARIANT THROUGH THE COMBINED    
JRNL        TITL 3 USE OF CHEMICAL BIOLOGY AND X-RAY CRYSTALLOGRAPHY.           
JRNL        REF    BIOCHEMISTRY                  V.  59   955 2020              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   31999437                                                     
JRNL        DOI    10.1021/ACS.BIOCHEM.9B01072                                  
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.90 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX                                               
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 23.29                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 89.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 29735                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.177                           
REMARK   3   R VALUE            (WORKING SET) : 0.174                           
REMARK   3   FREE R VALUE                     : 0.211                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 6.680                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1985                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 23.2867 -  4.5602    0.96     2181   157  0.1493 0.1747        
REMARK   3     2  4.5602 -  3.6240    0.97     2150   154  0.1400 0.1700        
REMARK   3     3  3.6240 -  3.1672    0.96     2128   153  0.1579 0.2008        
REMARK   3     4  3.1672 -  2.8782    0.93     2097   149  0.1985 0.2326        
REMARK   3     5  2.8782 -  2.6722    0.92     2025   145  0.2051 0.2383        
REMARK   3     6  2.6722 -  2.5148    0.93     2059   149  0.2071 0.2665        
REMARK   3     7  2.5148 -  2.3890    0.93     2079   146  0.2060 0.2471        
REMARK   3     8  2.3890 -  2.2851    0.94     2087   149  0.1958 0.2293        
REMARK   3     9  2.2851 -  2.1972    0.93     2010   144  0.1886 0.2445        
REMARK   3    10  2.1972 -  2.1215    0.93     2057   147  0.1895 0.2193        
REMARK   3    11  2.1215 -  2.0552    0.92     2032   145  0.1888 0.2159        
REMARK   3    12  2.0552 -  1.9964    0.91     2033   146  0.2050 0.2495        
REMARK   3    13  1.9964 -  1.9439    0.77     1679   120  0.2109 0.2917        
REMARK   3    14  1.9439 -  1.8965    0.51     1133    81  0.2547 0.2767        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.200            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.550           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 32.16                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.007           3420                                  
REMARK   3   ANGLE     :  0.894           4743                                  
REMARK   3   CHIRALITY :  0.048            516                                  
REMARK   3   PLANARITY :  0.005            502                                  
REMARK   3   DIHEDRAL  : 17.866           1963                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6NKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-19.                  
REMARK 100 THE DEPOSITION ID IS D_1000238861.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 17-JUL-17                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU MICROMAX-007                
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : VIRAMAX                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU SATURN 944                  
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 29961                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.900                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 90.3                               
REMARK 200  DATA REDUNDANCY                : 3.200                              
REMARK 200  R MERGE                    (I) : 0.04600                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 19.3000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.93                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 52.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.30                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.31600                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHENIX                                                
REMARK 200 STARTING MODEL: 2FMS                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 46.02                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18% PEG 3350, 350 MM SODIUM           
REMARK 280  ACETATE, 50 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP,    
REMARK 280  TEMPERATURE 291K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y+1/2,-Z                                             
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       39.88200            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC                        
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC                 
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 6840 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 19720 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL                       
REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, A                            
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MET A     1                                                      
REMARK 465     SER A     2                                                      
REMARK 465     LYS A     3                                                      
REMARK 465     ARG A     4                                                      
REMARK 465     LYS A     5                                                      
REMARK 465     ALA A     6                                                      
REMARK 465     PRO A     7                                                      
REMARK 465     GLN A     8                                                      
REMARK 465     GLU A     9                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     VAL A 303    CG1  CG2                                            
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   OE2  GLU A   153     O    HOH A   501              1.80            
REMARK 500   O    HOH A   702     O    HOH A   734              1.81            
REMARK 500   O    HOH A   775     O    HOH A   790              1.89            
REMARK 500   O    HOH T   230     O    HOH P   219              2.03            
REMARK 500   O    HOH A   761     O    HOH A   786              2.04            
REMARK 500   OG1  THR A   304     O    HOH A   502              2.06            
REMARK 500   O    HOH T   242     O    HOH P   213              2.06            
REMARK 500   O    HOH P   222     O    HOH A   807              2.08            
REMARK 500   OP2   DT P     6     O    HOH P   201              2.08            
REMARK 500   O    HOH P   220     O    HOH A   762              2.08            
REMARK 500   O    HOH A   567     O    HOH A   787              2.16            
REMARK 500   O    HOH A   742     O    HOH A   767              2.17            
REMARK 500   O    HOH A   720     O    HOH A   733              2.17            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500   O    HOH A   596     O    HOH A   792     2655     2.06            
REMARK 500   O    HOH A   709     O    HOH A   782     2555     2.11            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
REMARK 500     DT D   1   P      DT D   1   OP3    -0.119                       
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500     DA T   5   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500     DA T   8   O4' -  C1' -  N9  ANGL. DEV. =   1.8 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    CYS A 178     -138.16   -112.47                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA P 101  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DT P   9   OP1                                                    
REMARK 620 2 THR A 101   O   164.3                                              
REMARK 620 3 VAL A 103   O    94.9  95.1                                        
REMARK 620 4 ILE A 106   O    94.3  97.6  91.2                                  
REMARK 620 5 HOH P 203   O    84.5  85.1 178.0  90.8                            
REMARK 620 N                    1     2     3     4                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA D 101  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DC D   3   OP1                                                    
REMARK 620 2 LYS A  60   O   168.7                                              
REMARK 620 3 LEU A  62   O    96.7  94.6                                        
REMARK 620 4 VAL A  65   O    86.9  90.1 100.4                                  
REMARK 620 5 HOH A 744   O    94.2  88.4  81.6 177.6                            
REMARK 620 6 HOH D 204   O    72.0  97.1 164.8  89.3  89.0                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 401  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP A 190   OD1                                                    
REMARK 620 2 ASP A 192   OD2  95.3                                              
REMARK 620 3 DGT A 407   O1B 176.2  88.1                                        
REMARK 620 4 DGT A 407   O1A  94.5  91.9  87.0                                  
REMARK 620 5 DGT A 407   O1G  93.6 171.0  83.0  87.6                            
REMARK 620 6 HOH A 599   O    91.8  84.6  86.9 173.0  94.9                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A 402  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP A 190   OD1                                                    
REMARK 620 2 ASP A 190   OD2  47.6                                              
REMARK 620 3 ASP A 192   OD1  84.2 130.1                                        
REMARK 620 4 ASP A 256   OD2 130.8 106.1  95.8                                  
REMARK 620 5 DGT A 407   O1A  69.0  84.7  89.6 159.9                            
REMARK 620 N                    1     2     3     4                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG T 101  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH D 210   O                                                      
REMARK 620 2 HOH T 209   O   100.6                                              
REMARK 620 3 HOH T 239   O   166.3  93.0                                        
REMARK 620 4 HOH A 778   O    88.6  94.2  91.8                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue MG T 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NA P 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC5                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC6                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC7                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 404                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC8                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC9                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 406                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AD1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue DGT A 407                 
DBREF  6NKU T    1    16  PDB    6NKU     6NKU             1     16             
DBREF  6NKU P    1    10  PDB    6NKU     6NKU             1     10             
DBREF  6NKU D    1     5  PDB    6NKU     6NKU             1      5             
DBREF  6NKU A    1   335  UNP    P06746   DPOLB_HUMAN      1    335             
SEQRES   1 T   16   DC  DC  DG  DA  DA  DC  DA  DA  DG  DC  DA  DT  DC          
SEQRES   2 T   16   DA  DG  DC                                                  
SEQRES   1 P   10   DG  DC  DT  DG  DA  DT  DG  DC  DT 2DT                      
SEQRES   1 D    5   DT  DT  DC  DG  DG                                          
SEQRES   1 A  335  MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY          
SEQRES   2 A  335  GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU          
SEQRES   3 A  335  LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR          
SEQRES   4 A  335  ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS          
SEQRES   5 A  335  ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL          
SEQRES   6 A  335  GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA          
SEQRES   7 A  335  THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP          
SEQRES   8 A  335  ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER          
SEQRES   9 A  335  GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU          
SEQRES  10 A  335  GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP          
SEQRES  11 A  335  LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE          
SEQRES  12 A  335  GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU          
SEQRES  13 A  335  GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL          
SEQRES  14 A  335  ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG          
SEQRES  15 A  335  ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU          
SEQRES  16 A  335  THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO          
SEQRES  17 A  335  LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL          
SEQRES  18 A  335  HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS          
SEQRES  19 A  335  PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU          
SEQRES  20 A  335  LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE          
SEQRES  21 A  335  PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR          
SEQRES  22 A  335  GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA          
SEQRES  23 A  335  LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG          
SEQRES  24 A  335  PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO          
SEQRES  25 A  335  VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP          
SEQRES  26 A  335  LYS TYR ARG GLU PRO LYS ASP ARG SER GLU                      
HET    2DT  P  10      19                                                       
HET     MG  T 101       1                                                       
HET     NA  P 101       1                                                       
HET     NA  D 101       1                                                       
HET     MG  A 401       1                                                       
HET     NA  A 402       1                                                       
HET     CL  A 403       1                                                       
HET     CL  A 404       1                                                       
HET     CL  A 405       1                                                       
HET     CL  A 406       1                                                       
HET    DGT  A 407      31                                                       
HETNAM     2DT 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE                               
HETNAM      MG MAGNESIUM ION                                                    
HETNAM      NA SODIUM ION                                                       
HETNAM      CL CHLORIDE ION                                                     
HETNAM     DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE                                
HETSYN     2DT 2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE                          
FORMUL   2  2DT    C10 H15 N2 O7 P                                              
FORMUL   5   MG    2(MG 2+)                                                     
FORMUL   6   NA    3(NA 1+)                                                     
FORMUL  10   CL    4(CL 1-)                                                     
FORMUL  14  DGT    C10 H16 N5 O13 P3                                            
FORMUL  15  HOH   *394(H2 O)                                                    
HELIX    1 AA1 ASN A   12  VAL A   29  1                                  18    
HELIX    2 AA2 ALA A   32  TYR A   49  1                                  18    
HELIX    3 AA3 SER A   55  LYS A   61  1                                   7    
HELIX    4 AA4 GLY A   66  GLY A   80  1                                  15    
HELIX    5 AA5 LEU A   82  ASP A   91  1                                  10    
HELIX    6 AA6 ASP A   91  THR A  101  1                                  11    
HELIX    7 AA7 GLY A  107  GLU A  117  1                                  11    
HELIX    8 AA8 THR A  121  ASN A  128  1                                   8    
HELIX    9 AA9 GLU A  129  LEU A  132  5                                   4    
HELIX   10 AB1 ASN A  133  TYR A  142  1                                  10    
HELIX   11 AB2 TYR A  142  LYS A  148  1                                   7    
HELIX   12 AB3 ARG A  152  ASP A  170  1                                  19    
HELIX   13 AB4 CYS A  178  ARG A  183  1                                   6    
HELIX   14 AB5 LYS A  209  VAL A  221  1                                  13    
HELIX   15 AB6 PRO A  261  ASP A  263  5                                   3    
HELIX   16 AB7 GLN A  264  GLY A  274  1                                  11    
HELIX   17 AB8 SER A  275  LYS A  289  1                                  15    
HELIX   18 AB9 SER A  315  ILE A  323  1                                   9    
HELIX   19 AC1 GLU A  329  ARG A  333  5                                   5    
SHEET    1 AA1 2 ILE A 150  PRO A 151  0                                        
SHEET    2 AA1 2 SER A 187  SER A 188 -1  O  SER A 188   N  ILE A 150           
SHEET    1 AA2 5 ILE A 174  VAL A 177  0                                        
SHEET    2 AA2 5 MET A 191  THR A 196 -1  O  LEU A 194   N  THR A 176           
SHEET    3 AA2 5 ARG A 253  LEU A 259  1  O  ARG A 258   N  LEU A 195           
SHEET    4 AA2 5 LYS A 234  CYS A 239 -1  N  CYS A 239   O  ARG A 253           
SHEET    5 AA2 5 ILE A 224  LYS A 230 -1  N  LEU A 228   O  MET A 236           
SHEET    1 AA3 2 PHE A 291  ILE A 293  0                                        
SHEET    2 AA3 2 ILE A 298  PRO A 300 -1  O  ARG A 299   N  THR A 292           
LINK         OP1  DT P   9                NA    NA P 101     1555   1555  2.39  
LINK         O3'  DT P   9                 P   2DT P  10     1555   1555  1.60  
LINK         OP1  DC D   3                NA    NA D 101     1555   1555  2.61  
LINK         O   LYS A  60                NA    NA D 101     1555   1555  2.41  
LINK         O   LEU A  62                NA    NA D 101     1555   1555  2.28  
LINK         O   VAL A  65                NA    NA D 101     1555   1555  2.36  
LINK         O   THR A 101                NA    NA P 101     1555   1555  2.29  
LINK         O   VAL A 103                NA    NA P 101     1555   1555  2.44  
LINK         O   ILE A 106                NA    NA P 101     1555   1555  2.30  
LINK         OD1 ASP A 190                MG    MG A 401     1555   1555  2.02  
LINK         OD1 ASP A 190                NA    NA A 402     1555   1555  2.95  
LINK         OD2 ASP A 190                NA    NA A 402     1555   1555  2.18  
LINK         OD1 ASP A 192                NA    NA A 402     1555   1555  2.23  
LINK         OD2 ASP A 192                MG    MG A 401     1555   1555  2.09  
LINK         OD2 ASP A 256                NA    NA A 402     1555   1555  2.23  
LINK        MG    MG T 101                 O   HOH D 210     1555   1555  2.06  
LINK        MG    MG T 101                 O   HOH T 209     1555   1555  1.87  
LINK        MG    MG T 101                 O   HOH T 239     1555   1555  2.21  
LINK        MG    MG T 101                 O   HOH A 778     1555   1555  2.24  
LINK        NA    NA P 101                 O   HOH P 203     1555   1555  2.54  
LINK        NA    NA D 101                 O   HOH A 744     1555   1555  2.47  
LINK        NA    NA D 101                 O   HOH D 204     1555   1555  2.66  
LINK        MG    MG A 401                 O1B DGT A 407     1555   1555  2.11  
LINK        MG    MG A 401                 O1A DGT A 407     1555   1555  2.18  
LINK        MG    MG A 401                 O1G DGT A 407     1555   1555  2.06  
LINK        MG    MG A 401                 O   HOH A 599     1555   1555  2.17  
LINK        NA    NA A 402                 O1A DGT A 407     1555   1555  2.46  
CISPEP   1 GLY A  274    SER A  275          0         1.20                     
SITE     1 AC1  4 HOH A 778  HOH D 210  HOH T 209  HOH T 239                    
SITE     1 AC2  5 THR A 101  VAL A 103  ILE A 106   DT P   9                    
SITE     2 AC2  5 HOH P 203                                                     
SITE     1 AC3  6 LYS A  60  LEU A  62  VAL A  65  HOH A 744                    
SITE     2 AC3  6  DC D   3  HOH D 204                                          
SITE     1 AC4  5 ASP A 190  ASP A 192   NA A 402  DGT A 407                    
SITE     2 AC4  5 HOH A 599                                                     
SITE     1 AC5  6 ASP A 190  ASP A 192  ASP A 256   MG A 401                    
SITE     2 AC5  6 DGT A 407  2DT P  10                                          
SITE     1 AC6  5 GLN A 264  TYR A 266  CYS A 267  VAL A 313                    
SITE     2 AC6  5 HOH A 568                                                     
SITE     1 AC7  4 ALA A  32  ILE A  33  HIS A  34  LYS A  35                    
SITE     1 AC8  2 LEU A  82  ARG A  89                                          
SITE     1 AC9  3 ASN A 294  THR A 297  ARG A 299                               
SITE     1 AD1 27 GLY A 179  SER A 180  ARG A 183  SER A 188                    
SITE     2 AD1 27 GLY A 189  ASP A 190  ASP A 192  TYR A 271                    
SITE     3 AD1 27 PHE A 272  THR A 273  GLY A 274  ASP A 276                    
SITE     4 AD1 27 ASN A 279  ARG A 283   MG A 401   NA A 402                    
SITE     5 AD1 27 HOH A 539  HOH A 566  HOH A 599  HOH A 605                    
SITE     6 AD1 27 HOH A 618  HOH A 672  HOH A 717  HOH A 743                    
SITE     7 AD1 27 2DT P  10   DC T   6   DA T   7                               
CRYST1   50.630   79.764   55.378  90.00 107.69  90.00 P 1 21 1      2          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.019751  0.000000  0.006300        0.00000                         
SCALE2      0.000000  0.012537  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.018954        0.00000