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Database: PDB
Entry: 2D8M
LinkDB: 2D8M
Original site: 2D8M 
HEADER    DNA BINDING PROTEIN                     06-DEC-05   2D8M              
TITLE     SOLUTION STRUCTURE OF THE FIRST BRCT DOMAIN OF DNA-REPAIR             
TITLE    2 PROTEIN XRCC1                                                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA-REPAIR PROTEIN XRCC1;                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: BRCT DOMAIN;                                               
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: XRCC1;                                                         
SOURCE   6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   7 EXPRESSION_SYSTEM_PLASMID: P050322-07;                               
SOURCE   8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS                           
KEYWDS    PARALLEL BETA-SHEET, DNA LIGASE III, POLY(ADP-RIBOSE)                 
KEYWDS   2 POLYMERASE-1, DNA POLYMERASE BETA, STRUCTURAL GENOMICS,              
KEYWDS   3 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND                   
KEYWDS   4 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS            
KEYWDS   5 INITIATIVE, RSGI, DNA BINDING PROTEIN                                
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL                     
AUTHOR   2 GENOMICS/PROTEOMICS INITIATIVE (RSGI)                                
REVDAT   2   24-FEB-09 2D8M    1       VERSN                                    
REVDAT   1   06-JUN-06 2D8M    0                                                
JRNL        AUTH   T.NAGASHIMA,F.HAYASHI,S.YOKOYAMA                             
JRNL        TITL   SOLUTION STRUCTURE OF THE FIRST BRCT DOMAIN OF               
JRNL        TITL 2 DNA-REPAIR PROTEIN XRCC1                                     
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CYANA 2.0.17                                         
REMARK   3   AUTHORS     : GUNTERT, P.                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2D8M COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-05.                  
REMARK 100 THE RCSB ID CODE IS RCSB025123.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 293                                
REMARK 210  PH                             : 7.0                                
REMARK 210  IONIC STRENGTH                 : 120MM                              
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.89MM BRCT DOMAIN U-15N,13C;      
REMARK 210                                   20MM TRISHCL, 100MM NACL, 1MM      
REMARK 210                                   DTT, 0.02% NAN3; 90% H2O, 10%      
REMARK 210                                   D2O                                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_        
REMARK 210                                   15N-SEPARATED_NOESY                
REMARK 210  SPECTROMETER FIELD STRENGTH    : 900 MHZ, 800 MHZ                   
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : VNMR 6.1C, NMRPIPE 20020425,       
REMARK 210                                   NMRVIEW 5.0.4, KUJIRA 0.901,       
REMARK 210                                   CYANA 2.0.17                       
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS             
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : TARGET FUNCTION,STRUCTURES         
REMARK 210                                   WITH THE LOWEST ENERGY             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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  1 ARG A  13      164.40    -45.88                                   
REMARK 500  1 PRO A  16        0.58    -69.74                                   
REMARK 500  1 ALA A  68     -177.04    -66.44                                   
REMARK 500  1 SER A 112       48.50    -87.89                                   
REMARK 500  1 SER A 124       44.11    -81.49                                   
REMARK 500  1 PRO A 126        2.80    -69.77                                   
REMARK 500  1 SER A 128       87.65    -59.63                                   
REMARK 500  2 GLU A   8       66.18   -117.88                                   
REMARK 500  2 ALA A  14       43.69    -80.80                                   
REMARK 500  2 LEU A  23       41.49   -104.87                                   
REMARK 500  2 GLU A  87      -32.07    -35.93                                   
REMARK 500  2 PRO A 109       86.93    -69.76                                   
REMARK 500  2 ASP A 116      137.20    -39.29                                   
REMARK 500  2 HIS A 120      -35.15    -37.20                                   
REMARK 500  3 SER A   3       41.07    -98.14                                   
REMARK 500  3 PRO A  12        0.12    -69.71                                   
REMARK 500  3 ARG A  13      113.87    -38.54                                   
REMARK 500  3 CYS A  92      -36.78    -35.08                                   
REMARK 500  3 SER A 113       42.44   -100.78                                   
REMARK 500  4 TRP A  56      107.59    -53.68                                   
REMARK 500  4 ALA A  68     -179.89    -69.83                                   
REMARK 500  4 PRO A 100       99.03    -69.77                                   
REMARK 500  4 SER A 119      127.90    -35.81                                   
REMARK 500  4 SER A 128      135.08    -34.74                                   
REMARK 500  5 ALA A  14       40.87   -102.11                                   
REMARK 500  5 TRP A  56       89.40    -62.44                                   
REMARK 500  5 ALA A  68     -175.56    -68.27                                   
REMARK 500  5 GLU A  87      -26.47    -38.65                                   
REMARK 500  5 CYS A  92      -33.64    -34.57                                   
REMARK 500  5 ARG A  96       35.61     70.89                                   
REMARK 500  5 SER A 111       73.49   -108.33                                   
REMARK 500  5 GLU A 114       78.37   -113.90                                   
REMARK 500  5 ALA A 118      106.83   -163.12                                   
REMARK 500  6 PRO A  16        2.51    -69.71                                   
REMARK 500  6 ALA A  68     -175.07    -64.50                                   
REMARK 500  6 SER A 112      -60.72   -100.17                                   
REMARK 500  7 SER A   2      139.19   -170.74                                   
REMARK 500  7 ARG A  11      139.21    -34.57                                   
REMARK 500  7 LEU A  23       40.97   -105.08                                   
REMARK 500  7 ALA A  68     -178.94    -57.05                                   
REMARK 500  7 SER A 119       89.24    -68.22                                   
REMARK 500  7 PRO A 126     -174.31    -69.77                                   
REMARK 500  8 PRO A  16        2.03    -69.75                                   
REMARK 500  8 LEU A  23       56.37   -106.23                                   
REMARK 500  8 PRO A 109       89.24    -69.76                                   
REMARK 500  8 SER A 113       49.55     36.52                                   
REMARK 500  8 ALA A 118       43.02   -108.47                                   
REMARK 500  8 SER A 128       42.26    -96.08                                   
REMARK 500  9 ARG A  13      173.45    -47.22                                   
REMARK 500  9 ALA A  14       33.21    -85.05                                   
REMARK 500  9 TRP A  56      105.49    -57.27                                   
REMARK 500  9 ALA A  68     -178.07    -66.53                                   
REMARK 500  9 LEU A  90      -71.36    -42.51                                   
REMARK 500  9 SER A 112       43.97    -82.07                                   
REMARK 500  9 ALA A 118      -61.66   -101.52                                   
REMARK 500  9 PRO A 126       88.35    -69.69                                   
REMARK 500 10 ALA A  14       74.78    -64.41                                   
REMARK 500 10 LEU A  23       57.30   -106.76                                   
REMARK 500 10 SER A  60      106.36    -51.80                                   
REMARK 500 10 ALA A  68     -175.40    -60.71                                   
REMARK 500 10 PRO A 100       93.40    -69.78                                   
REMARK 500 10 MET A 106      -61.72    -90.62                                   
REMARK 500 10 PRO A 109     -172.95    -69.73                                   
REMARK 500 10 SER A 111       77.16    -61.56                                   
REMARK 500 10 SER A 113       39.22    -92.55                                   
REMARK 500 10 ALA A 118       80.61    -66.47                                   
REMARK 500 10 HIS A 120      105.12    -44.93                                   
REMARK 500 10 SER A 127      117.00    -39.45                                   
REMARK 500 11 PRO A  12     -174.64    -69.79                                   
REMARK 500 11 PRO A  16        2.33    -69.83                                   
REMARK 500 11 LEU A  23       47.91   -109.38                                   
REMARK 500 11 TRP A  56       99.95    -63.94                                   
REMARK 500 11 ALA A  68     -177.88    -68.84                                   
REMARK 500 11 LEU A 105      108.17    -45.18                                   
REMARK 500 11 GLU A 114       41.09    -95.32                                   
REMARK 500 11 GLU A 115      176.29    -57.52                                   
REMARK 500 12 GLU A   8       96.00    -32.66                                   
REMARK 500 12 PRO A   9       92.43    -69.83                                   
REMARK 500 12 SER A 111       97.32    -64.31                                   
REMARK 500 12 SER A 112       38.92    -94.07                                   
REMARK 500 12 ALA A 118      116.56   -161.78                                   
REMARK 500 13 ARG A  10       51.64   -114.61                                   
REMARK 500 13 PRO A  16        2.53    -69.82                                   
REMARK 500 13 ALA A  68     -178.00    -68.44                                   
REMARK 500 13 LEU A 105      107.51    -52.77                                   
REMARK 500 13 PRO A 109       88.31    -69.72                                   
REMARK 500 13 SER A 113       40.54     37.60                                   
REMARK 500 13 ASP A 116      151.89    -47.18                                   
REMARK 500 13 GLU A 117      -56.33   -131.40                                   
REMARK 500 14 GLU A   8      143.74   -172.66                                   
REMARK 500 14 ARG A  38      -70.02    -51.23                                   
REMARK 500 14 ALA A  68     -175.02    -68.55                                   
REMARK 500 15 PRO A  16        1.73    -69.82                                   
REMARK 500 15 ARG A  85     -176.91    -59.20                                   
REMARK 500 15 TRP A  88      -71.24    -36.25                                   
REMARK 500 15 SER A 111       80.34    -57.43                                   
REMARK 500 15 ALA A 118      137.85   -172.85                                   
REMARK 500 15 SER A 121       90.11    -66.54                                   
REMARK 500 16 SER A   5      119.11   -166.48                                   
REMARK 500 16 PRO A   9       82.83    -69.70                                   
REMARK 500 16 PRO A  16        2.19    -69.73                                   
REMARK 500 16 LEU A  23       43.55   -107.95                                   
REMARK 500 16 TRP A  56      109.96    -54.54                                   
REMARK 500 16 ALA A  68     -179.47    -64.64                                   
REMARK 500 16 SER A 112       78.05   -103.93                                   
REMARK 500 16 ALA A 118      117.08   -171.66                                   
REMARK 500 16 SER A 128       42.19     39.34                                   
REMARK 500 17 PRO A   9     -174.41    -69.76                                   
REMARK 500 17 TRP A  56       79.48    -64.99                                   
REMARK 500 17 ALA A  68     -178.60    -63.28                                   
REMARK 500 17 SER A 113       50.70   -118.61                                   
REMARK 500 17 GLU A 114       35.01    -83.92                                   
REMARK 500 17 ALA A 118      110.80   -169.87                                   
REMARK 500 17 SER A 127       53.81    -91.65                                   
REMARK 500 18 ALA A  14       35.10    -95.17                                   
REMARK 500 18 GLU A  17      -61.00    -93.00                                   
REMARK 500 18 GLU A  18      -38.88    -34.64                                   
REMARK 500 18 PHE A  37      -50.30    -29.17                                   
REMARK 500 18 ALA A  68     -177.42    -64.86                                   
REMARK 500 18 TRP A  88      -70.93    -49.55                                   
REMARK 500 18 PRO A 100       99.23    -69.73                                   
REMARK 500 18 SER A 111       39.29    -88.07                                   
REMARK 500 18 SER A 113       51.21    -97.22                                   
REMARK 500 18 GLU A 114       39.53    -86.00                                   
REMARK 500 18 SER A 119       40.76    -93.78                                   
REMARK 500 18 SER A 128      -60.11   -103.97                                   
REMARK 500 19 PRO A   9        4.88    -69.75                                   
REMARK 500 19 ALA A  14     -176.49    -63.10                                   
REMARK 500 19 PRO A  16        2.20    -69.69                                   
REMARK 500 19 ALA A  68     -179.34    -68.36                                   
REMARK 500 19 SER A 112      104.37    -40.80                                   
REMARK 500 19 SER A 113       38.77     34.56                                   
REMARK 500 19 GLU A 117      -17.76    -49.22                                   
REMARK 500 19 ALA A 118      -37.58    -35.15                                   
REMARK 500 19 PRO A 126       98.34    -69.74                                   
REMARK 500 20 SER A   5      110.17   -173.59                                   
REMARK 500 20 PRO A  16        2.83    -69.77                                   
REMARK 500 20 ALA A  68     -179.18    -65.93                                   
REMARK 500 20 SER A 113       39.68    -83.89                                   
REMARK 500 20 GLU A 115      147.38    -37.47                                   
REMARK 500 20 PRO A 126       90.32    -69.74                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: HSK003000003.1   RELATED DB: TARGETDB                    
DBREF  2D8M A    8   123  UNP    P18887   XRCC1_HUMAN    305    420             
SEQADV 2D8M GLY A    1  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A    2  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A    3  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M GLY A    4  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A    5  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A    6  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M GLY A    7  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M GLN A  102  UNP  P18887    ARG   399 SEE REMARK 999                 
SEQADV 2D8M SER A  124  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M GLY A  125  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M PRO A  126  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A  127  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M SER A  128  UNP  P18887              CLONING ARTIFACT               
SEQADV 2D8M GLY A  129  UNP  P18887              CLONING ARTIFACT               
SEQRES   1 A  129  GLY SER SER GLY SER SER GLY GLU PRO ARG ARG PRO ARG          
SEQRES   2 A  129  ALA GLY PRO GLU GLU LEU GLY LYS ILE LEU GLN GLY VAL          
SEQRES   3 A  129  VAL VAL VAL LEU SER GLY PHE GLN ASN PRO PHE ARG SER          
SEQRES   4 A  129  GLU LEU ARG ASP LYS ALA LEU GLU LEU GLY ALA LYS TYR          
SEQRES   5 A  129  ARG PRO ASP TRP THR ARG ASP SER THR HIS LEU ILE CYS          
SEQRES   6 A  129  ALA PHE ALA ASN THR PRO LYS TYR SER GLN VAL LEU GLY          
SEQRES   7 A  129  LEU GLY GLY ARG ILE VAL ARG LYS GLU TRP VAL LEU ASP          
SEQRES   8 A  129  CYS HIS ARG MET ARG ARG ARG LEU PRO SER GLN ARG TYR          
SEQRES   9 A  129  LEU MET ALA GLY PRO GLY SER SER SER GLU GLU ASP GLU          
SEQRES  10 A  129  ALA SER HIS SER GLY GLY SER GLY PRO SER SER GLY              
HELIX    1   1 GLY A   15  GLY A   20  1                                   6    
HELIX    2   2 PRO A   36  LEU A   48  1                                  13    
HELIX    3   3 THR A   70  GLY A   80  1                                  11    
HELIX    4   4 LYS A   86  MET A   95  1                                  10    
HELIX    5   5 PRO A  100  LEU A  105  5                                   6    
SHEET    1   A 4 ALA A  50  ARG A  53  0                                        
SHEET    2   A 4 VAL A  26  SER A  31  1  N  VAL A  26   O  LYS A  51           
SHEET    3   A 4 HIS A  62  CYS A  65  1  O  ILE A  64   N  VAL A  29           
SHEET    4   A 4 ARG A  82  ARG A  85  1  O  ARG A  82   N  LEU A  63           
CISPEP   1 ASN A   35    PRO A   36          1        -0.06                     
CISPEP   2 ASN A   35    PRO A   36          2        -0.06                     
CISPEP   3 ASN A   35    PRO A   36          3        -0.08                     
CISPEP   4 ASN A   35    PRO A   36          4        -0.07                     
CISPEP   5 ASN A   35    PRO A   36          5        -0.16                     
CISPEP   6 ASN A   35    PRO A   36          6        -0.07                     
CISPEP   7 ASN A   35    PRO A   36          7        -0.02                     
CISPEP   8 ASN A   35    PRO A   36          8        -0.05                     
CISPEP   9 ASN A   35    PRO A   36          9        -0.04                     
CISPEP  10 ASN A   35    PRO A   36         10        -0.01                     
CISPEP  11 ASN A   35    PRO A   36         11        -0.07                     
CISPEP  12 ASN A   35    PRO A   36         12        -0.10                     
CISPEP  13 ASN A   35    PRO A   36         13        -0.07                     
CISPEP  14 ASN A   35    PRO A   36         14         0.01                     
CISPEP  15 ASN A   35    PRO A   36         15        -0.05                     
CISPEP  16 ASN A   35    PRO A   36         16        -0.02                     
CISPEP  17 ASN A   35    PRO A   36         17        -0.10                     
CISPEP  18 ASN A   35    PRO A   36         18        -0.06                     
CISPEP  19 ASN A   35    PRO A   36         19        -0.10                     
CISPEP  20 ASN A   35    PRO A   36         20        -0.05                     
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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