PDB Short entry for 1BF4
HEADER    DNA-BINDING PROTEIN/DNA                 27-MAY-98   1BF4              
TITLE     CHROMOSOMAL DNA-BINDING PROTEIN SSO7D/D(GCGAACGC) COMPLEX             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*CP*GP*TP*5IUP*CP*GP*C)-3');                  
COMPND   3 CHAIN: B;                                                            
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MOL_ID: 2;                                                           
COMPND   6 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*AP*CP*GP*C)-3');                    
COMPND   7 CHAIN: C;                                                            
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 MOL_ID: 3;                                                           
COMPND  10 MOLECULE: PROTEIN (CHROMOSOMAL PROTEIN SSO7D);                       
COMPND  11 CHAIN: A;                                                            
COMPND  12 SYNONYM: DNA-BINDING PROTEIN 7D, 7 KD DNA-BINDING PROTEIN D, SSO7D;  
COMPND  13 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 MOL_ID: 2;                                                           
SOURCE   4 SYNTHETIC: YES;                                                      
SOURCE   5 MOL_ID: 3;                                                           
SOURCE   6 ORGANISM_SCIENTIFIC: SULFOLOBUS ACIDOCALDARIUS;                      
SOURCE   7 ORGANISM_TAXID: 2285;                                                
SOURCE   8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   9 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    DNA BINDING PROTEIN, HYPERTHERMOPHILE, ARCHAEBACTERIA, COMPLEX (DNA-  
KEYWDS   2 BINDING PROTEIN-DNA), DNA-BINDING PROTEIN-DNA COMPLEX                
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.SU,Y.-G.GAO,H.ROBINSON,S.PADMANABHAN,L.LIM,J.W.SHRIVER,A.H.-J.WANG  
REVDAT   4   22-NOV-17 1BF4    1       REMARK                                   
REVDAT   3   24-FEB-09 1BF4    1       VERSN                                    
REVDAT   2   01-APR-03 1BF4    1       JRNL                                     
REVDAT   1   10-NOV-99 1BF4    0                                                
JRNL        AUTH   Y.G.GAO,S.Y.SU,H.ROBINSON,S.PADMANABHAN,L.LIM,B.S.MCCRARY,   
JRNL        AUTH 2 S.P.EDMONDSON,J.W.SHRIVER,A.H.WANG                           
JRNL        TITL   THE CRYSTAL STRUCTURE OF THE HYPERTHERMOPHILE CHROMOSOMAL    
JRNL        TITL 2 PROTEIN SSO7D BOUND TO DNA.                                  
JRNL        REF    NAT.STRUCT.BIOL.              V.   5   782 1998              
JRNL        REFN                   ISSN 1072-8368                               
JRNL        PMID   9731772                                                      
JRNL        DOI    10.1038/1822                                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.60 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.840                                         
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 6.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 10000000.000                   
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0010                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 95.1                           
REMARK   3   NUMBER OF REFLECTIONS             : 11256                          
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) : 0.211                           
REMARK   3   FREE R VALUE                     : 0.288                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.940                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1115                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.009                           
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) : 1.60                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.67                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 86.70                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1138                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3430                       
REMARK   3   BIN FREE R VALUE                    : 0.3770                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.30                        
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 130                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.033                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 502                                     
REMARK   3   NUCLEIC ACID ATOMS       : 322                                     
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 114                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 14.80                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 25.00                          
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.22                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.28                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 6.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.26                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.28                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.012                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.500                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 24.00                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.600                           
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) : 1.920 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 3.040 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.680 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 3.760 ; 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  : PARAM_NDBX_HIGH.DNA                            
REMARK   3  PARAMETER FILE  2  : NEW.PAM                                        
REMARK   3  PARAMETER FILE  3  : PARAM11.WAT                                    
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : TOPH11.WAT                                     
REMARK   3  TOPOLOGY FILE  2   : TOP_NDBX.DNA                                   
REMARK   3  TOPOLOGY FILE  3   : NEW.TOP                                        
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1BF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB.                               
REMARK 100 THE DEPOSITION ID IS D_1000171680.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-JUL-97                          
REMARK 200  TEMPERATURE           (KELVIN) : 123                                
REMARK 200  PH                             : 6.5                                
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 RU200                       
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : GRAPHITE                           
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU                             
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : BIOTEX V. 1.1                      
REMARK 200  DATA SCALING SOFTWARE          : BIOTEX V. 1.1                      
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 11595                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 6.000                              
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.1                               
REMARK 200  DATA REDUNDANCY                : 4.360                              
REMARK 200  R MERGE                    (I) : 0.07370                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 15.0000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.65                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 86.6                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.27800                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 2.400                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: AMORE                                                 
REMARK 200 STARTING MODEL: SSO7D-GTAATTAC                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 39.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5                                   
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       23.43500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       18.82500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       24.83500            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       18.82500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       23.43500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       24.83500            
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: TRIMERIC                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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    ASP A  50      -70.33    -64.50                                   
REMARK 500    ALA A  51      104.87      2.21                                   
REMARK 500    GLN A  62      -80.51   -124.32                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500     DC C 114         0.07    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1BF4 A    2    64  UNP    P13123   DN71_SULAC       1     63             
DBREF  1BF4 B  101   108  PDB    1BF4     1BF4           101    108             
DBREF  1BF4 C  109   116  PDB    1BF4     1BF4           109    116             
SEQRES   1 B    8   DG  DC  DG  DT 5IU  DC  DG  DC                              
SEQRES   1 C    8   DG  DC  DG  DA  DA  DC  DG  DC                              
SEQRES   1 A   63  ALA THR VAL LYS PHE LYS TYR LYS GLY GLU GLU LYS GLU          
SEQRES   2 A   63  VAL ASP ILE SER LYS ILE LYS LYS VAL TRP ARG VAL GLY          
SEQRES   3 A   63  LYS MET ILE SER PHE THR TYR ASP GLU GLY GLY GLY LYS          
SEQRES   4 A   63  THR GLY ARG GLY ALA VAL SER GLU LYS ASP ALA PRO LYS          
SEQRES   5 A   63  GLU LEU LEU GLN MET LEU GLU LYS GLN LYS LYS                  
MODRES 1BF4 5IU B  105   DU  5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE            
HET    5IU  B 105      20                                                       
HETNAM     5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE                          
FORMUL   1  5IU    C9 H12 I N2 O8 P                                             
FORMUL   4  HOH   *114(H2 O)                                                    
HELIX    1   1 ILE A   17  LYS A   19  5                                   3    
HELIX    2   2 GLY A   37  GLY A   39  5                                   3    
HELIX    3   3 LYS A   53  LYS A   61  1                                   9    
SHEET    1   A 2 THR A   3  TYR A   8  0                                        
SHEET    2   A 2 GLU A  11  ASP A  16 -1  N  VAL A  15   O  VAL A   4           
SHEET    1   B 3 THR A  41  SER A  47  0                                        
SHEET    2   B 3 MET A  29  ASP A  35 -1  N  TYR A  34   O  GLY A  42           
SHEET    3   B 3 ILE A  20  VAL A  26 -1  N  VAL A  26   O  MET A  29           
LINK         O3' 5IU B 105                 P    DC B 106     1555   1555  1.60  
LINK         P   5IU B 105                 O3'  DT B 104     1555   1555  1.61  
CRYST1   46.870   49.670   37.650  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      0.021336  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.020133  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.026560        0.00000