PDB Short entry for 1AKZ
HEADER    GLYCOSIDASE                             27-MAY-97   1AKZ              
TITLE     HUMAN URACIL-DNA GLYCOSYLASE                                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: URACIL-DNA GLYCOSYLASE;                                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: UDG, UNG;                                                   
COMPND   5 EC: 3.2.2.-;                                                         
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MUTATION: YES;                                                       
COMPND   8 OTHER_DETAILS: STRUCTURE IS THAT OF RECOMBINANT HUMAN URACIL-DNA     
COMPND   9 GLYCOSYLASE IN WHICH THE 84 N-TERMINAL AMINO ACIDS CODED FOR BY THE  
COMPND  10 UNG GENE HAVE BEEN REPLACED BY THREE RESIDUES FROM THE EXPRESSION    
COMPND  11 VECTOR                                                               
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    GLYCOSYLASE, DNA REPAIR, URACIL REMOVAL FROM DNA, ALPHA/ BETA         
KEYWDS   2 PROTEIN, GLYCOSIDASE                                                 
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.A.TAINER,C.D.MOL                                                    
REVDAT   3   30-MAR-11 1AKZ    1       AUTHOR                                   
REVDAT   2   24-FEB-09 1AKZ    1       VERSN                                    
REVDAT   1   20-AUG-97 1AKZ    0                                                
JRNL        AUTH   S.S.PARIKH,C.D.MOL,G.SLUPPHAUG,S.BHARATI,H.E.KROKAN,         
JRNL        AUTH 2 J.A.TAINER                                                   
JRNL        TITL   BASE EXCISION REPAIR INITIATION REVEALED BY CRYSTAL          
JRNL        TITL 2 STRUCTURES AND BINDING KINETICS OF HUMAN URACIL-DNA          
JRNL        TITL 3 GLYCOSYLASE WITH DNA.                                        
JRNL        REF    EMBO J.                       V.  17  5214 1998              
JRNL        REFN                   ISSN 0261-4189                               
JRNL        PMID   9724657                                                      
JRNL        DOI    10.1093/EMBOJ/17.17.5214                                     
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.57 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.8                                           
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 100000.000                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.1000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 94.5                           
REMARK   3   NUMBER OF REFLECTIONS             : 30381                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.189                           
REMARK   3   FREE R VALUE                     : 0.224                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.490                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 3048                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 8                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.57                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.64                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.70                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 3319                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3180                       
REMARK   3   BIN FREE R VALUE                    : 0.2860                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 9.85                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 390                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1808                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 185                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 4.90220                                              
REMARK   3    B22 (A**2) : 0.78850                                              
REMARK   3    B33 (A**2) : -5.69080                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.009                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.15                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.96                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.95                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : 0.958 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 1.649 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 1.746 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 2.812 ; 2.500                
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : PARHCSDX.PRO                                   
REMARK   3  PARAMETER FILE  2  : PARAM19.SOL                                    
REMARK   3  PARAMETER FILE  3  : NULL                                           
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : TOPHCSDX.PRO                                   
REMARK   3  TOPOLOGY FILE  2   : TOPH19.SOL                                     
REMARK   3  TOPOLOGY FILE  3   : TOPH19.PEP                                     
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: AN OVERALL BULK SOLVENT CORRECTION WAS    
REMARK   3  APPLIED TO THE DATA.                                                
REMARK   4                                                                      
REMARK   4 1AKZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : FEB-95                             
REMARK 200  TEMPERATURE           (KELVIN) : 275                                
REMARK 200  PH                             : 7.9                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL7-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.08                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : NULL                               
REMARK 200  DETECTOR MANUFACTURER          : NULL                               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 30433                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.570                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.5                               
REMARK 200  DATA REDUNDANCY                : 4.000                              
REMARK 200  R MERGE                    (I) : 0.04600                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 14.9000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.61                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.10600                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 11.000                             
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: NULL                                           
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS         
REMARK 200  REPLACEMENT                                                         
REMARK 200 SOFTWARE USED: PHASES, SQUASH, XTALVIEW                              
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM IMIDAZOLE/MALEATE, PH 7.9, 1%-    
REMARK 280  4% SATURATED NACL, 1%-4% SATURATED AMMONIUM SULFATE, 16%-20% PEG    
REMARK 280  4000, MIXED WITH EQUAL VOLUMES 30 MG/ML PROTEIN.                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-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       23.88000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       42.48500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       27.63500            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       42.48500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       23.88000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       27.63500            
REMARK 290   SMTRY3   4  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: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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    GLN A 144      -71.94   -109.25                                   
REMARK 500    HIS A 154       25.56   -140.45                                   
REMARK 500    PHE A 158      -16.92     67.34                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1AKZ A   85   304  UNP    P13051   UNG_HUMAN       85    304             
SEQRES   1 A  223  MET GLU PHE PHE GLY GLU SER TRP LYS LYS HIS LEU SER          
SEQRES   2 A  223  GLY GLU PHE GLY LYS PRO TYR PHE ILE LYS LEU MET GLY          
SEQRES   3 A  223  PHE VAL ALA GLU GLU ARG LYS HIS TYR THR VAL TYR PRO          
SEQRES   4 A  223  PRO PRO HIS GLN VAL PHE THR TRP THR GLN MET CYS ASP          
SEQRES   5 A  223  ILE LYS ASP VAL LYS VAL VAL ILE LEU GLY GLN ASP PRO          
SEQRES   6 A  223  TYR HIS GLY PRO ASN GLN ALA HIS GLY LEU CYS PHE SER          
SEQRES   7 A  223  VAL GLN ARG PRO VAL PRO PRO PRO PRO SER LEU GLU ASN          
SEQRES   8 A  223  ILE TYR LYS GLU LEU SER THR ASP ILE GLU ASP PHE VAL          
SEQRES   9 A  223  HIS PRO GLY HIS GLY ASP LEU SER GLY TRP ALA LYS GLN          
SEQRES  10 A  223  GLY VAL LEU LEU LEU ASN ALA VAL LEU THR VAL ARG ALA          
SEQRES  11 A  223  HIS GLN ALA ASN SER HIS LYS GLU ARG GLY TRP GLU GLN          
SEQRES  12 A  223  PHE THR ASP ALA VAL VAL SER TRP LEU ASN GLN ASN SER          
SEQRES  13 A  223  ASN GLY LEU VAL PHE LEU LEU TRP GLY SER TYR ALA GLN          
SEQRES  14 A  223  LYS LYS GLY SER ALA ILE ASP ARG LYS ARG HIS HIS VAL          
SEQRES  15 A  223  LEU GLN THR ALA HIS PRO SER PRO LEU SER VAL TYR ARG          
SEQRES  16 A  223  GLY PHE PHE GLY CYS ARG HIS PHE SER LYS THR ASN GLU          
SEQRES  17 A  223  LEU LEU GLN LYS SER GLY LYS LYS PRO ILE ASP TRP LYS          
SEQRES  18 A  223  GLU LEU                                                      
FORMUL   2  HOH   *185(H2 O)                                                    
HELIX    1   1 GLU A   87  GLY A   98  1                                  12    
HELIX    2   2 PRO A  100  HIS A  115  1                                  16    
HELIX    3   3 PRO A  122  GLN A  124  5                                   3    
HELIX    4   4 THR A  127  THR A  129  5                                   3    
HELIX    5   5 ILE A  134  ASP A  136  5                                   3    
HELIX    6   6 PRO A  168  ASP A  180  1                                  13    
HELIX    7   7 SER A  193  GLN A  198  1                                   6    
HELIX    8   8 TRP A  222  ASN A  236  1                                  15    
HELIX    9   9 SER A  247  ALA A  255  1                                   9    
HELIX   10  10 VAL A  274  ARG A  276  5                                   3    
HELIX   11  11 HIS A  283  SER A  294  1                                  12    
SHEET    1   A 4 VAL A 200  ASN A 204  0                                        
SHEET    2   A 4 VAL A 139  GLY A 143  1  N  VAL A 139   O  LEU A 201           
SHEET    3   A 4 VAL A 241  TRP A 245  1  N  VAL A 241   O  VAL A 140           
SHEET    4   A 4 HIS A 262  THR A 266  1  N  HIS A 262   O  PHE A 242           
CISPEP   1 TYR A  119    PRO A  120          0        -1.36                     
CISPEP   2 ARG A  162    PRO A  163          0         0.54                     
CRYST1   47.760   55.270   84.970  90.00  90.00  90.00 P 21 21 21    4          
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      0.020938  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.018093  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011769        0.00000