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Database: PDB
Entry: 2KEB
LinkDB: 2KEB
Original site: 2KEB 
HEADER    DNA BINDING PROTEIN                     28-JAN-09   2KEB              
TITLE     NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE DNA POLYMERASE 
TITLE    2 ALPHA P68 SUBUNIT                                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA POLYMERASE SUBUNIT ALPHA B;                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: DNA POLYMERASE ALPHA 70 KDA SUBUNIT;                        
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: POLA2;                                                         
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);                                
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PBG100                                    
KEYWDS    DNA POLYMERASE ALPHA, DNA REPLICATION, NUCLEUS, PHOSPHOPROTEIN, DNA   
KEYWDS   2 BINDING PROTEIN                                                      
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    H.HUANG,B.E.WEINER,H.ZHANG,B.E.FULLER,Y.GAO,B.M.WILE,W.J.CHAZIN,      
AUTHOR   2 E.FANNING                                                            
REVDAT   2   14-JUL-10 2KEB    1       JRNL                                     
REVDAT   1   02-FEB-10 2KEB    0                                                
JRNL        AUTH   H.HUANG,B.E.WEINER,H.ZHANG,B.E.FULLER,Y.GAO,B.M.WILE,K.ZHAO, 
JRNL        AUTH 2 D.R.ARNETT,W.J.CHAZIN,E.FANNING                              
JRNL        TITL   STRUCTURE OF A DNA POLYMERASE ALPHA-PRIMASE DOMAIN THAT      
JRNL        TITL 2 DOCKS ON THE SV40 HELICASE AND ACTIVATES THE VIRAL           
JRNL        TITL 3 PRIMOSOME.                                                   
JRNL        REF    J.BIOL.CHEM.                  V. 285 17112 2010              
JRNL        REFN                   ISSN 0021-9258                               
JRNL        PMID   20234039                                                     
JRNL        DOI    10.1074/JBC.M110.116830                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER 9                                              
REMARK   3   AUTHORS     : CASE, D. ET AL.                                      
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2KEB COMPLIES WITH FORMAT V. 3.20, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-09.                  
REMARK 100 THE RCSB ID CODE IS RCSB101014.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 0.05                               
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.75 MM [U-100% 13C; U-100% 15N]   
REMARK 210                                   PROTEIN, 95% H2O/5% D2O            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-1H NOESY; 3D 1H-15N NOESY;   
REMARK 210                                   3D 1H-13C NOESY; 4D 1H-13C NOESY   
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ; 600 MHZ; 500 MHZ          
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : CYANA 2.1                          
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LEAST          
REMARK 210                                   RESTRAINT VIOLATIONS               
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-20                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     MET A   -22                                                      
REMARK 465     GLY A   -21                                                      
REMARK 465     SER A   -20                                                      
REMARK 465     SER A   -19                                                      
REMARK 465     HIS A   -18                                                      
REMARK 465     HIS A   -17                                                      
REMARK 465     HIS A   -16                                                      
REMARK 465     HIS A   -15                                                      
REMARK 465     HIS A   -14                                                      
REMARK 465     HIS A   -13                                                      
REMARK 465     GLY A   -12                                                      
REMARK 465     SER A   -11                                                      
REMARK 465     SER A   -10                                                      
REMARK 465     LEU A    -9                                                      
REMARK 465     GLU A    -8                                                      
REMARK 465     VAL A    -7                                                      
REMARK 465     LEU A    -6                                                      
REMARK 465     PHE A    -5                                                      
REMARK 465     GLN A    -4                                                      
REMARK 465     GLY A    -3                                                      
REMARK 465     PRO A    -2                                                      
REMARK 465     GLY A    -1                                                      
REMARK 465     SER A     0                                                      
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  2 ARG A  78   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES          
REMARK 500  6 ARG A  78   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES          
REMARK 500 18 ARG A  78   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 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  1 SER A   4       96.19     78.15                                   
REMARK 500  1 PHE A  69      -45.49   -148.77                                   
REMARK 500  2 PHE A  69      -39.60   -153.36                                   
REMARK 500  2 ARG A  73      138.35     89.72                                   
REMARK 500  2 ALA A  77      -40.89   -153.25                                   
REMARK 500  3 ALA A   3       54.28   -163.16                                   
REMARK 500  3 PHE A  69      -44.45   -151.69                                   
REMARK 500  3 ARG A  73      141.45    167.28                                   
REMARK 500  4 ALA A   3      -73.76     62.71                                   
REMARK 500  4 SER A   4      147.86     80.35                                   
REMARK 500  4 HIS A  53        0.16     85.82                                   
REMARK 500  4 LEU A  57      164.63     69.72                                   
REMARK 500  4 PHE A  69      -43.03   -140.23                                   
REMARK 500  4 ARG A  73      138.12    174.46                                   
REMARK 500  4 ALA A  77      -41.72     69.99                                   
REMARK 500  5 ALA A   3      -60.59   -169.90                                   
REMARK 500  5 HIS A  53       20.59     83.09                                   
REMARK 500  5 PHE A  69      -42.72   -144.98                                   
REMARK 500  6 SER A   2       41.54    -84.71                                   
REMARK 500  6 PHE A  69      -49.71   -152.04                                   
REMARK 500  7 SER A   4      131.83     76.66                                   
REMARK 500  7 PHE A  48      -65.99    -94.43                                   
REMARK 500  7 PHE A  69      -48.42   -150.36                                   
REMARK 500  8 ASP A  18       46.92    -83.50                                   
REMARK 500  8 HIS A  53       32.11     71.89                                   
REMARK 500  8 PHE A  69      -43.96   -151.32                                   
REMARK 500  9 HIS A  53       47.50     72.96                                   
REMARK 500  9 VAL A  55       84.61     62.71                                   
REMARK 500 10 PHE A  69      -60.64   -154.87                                   
REMARK 500 10 ARG A  73      132.98    173.31                                   
REMARK 500 11 ASP A  18       43.51    -80.99                                   
REMARK 500 11 PHE A  69      -50.00   -147.72                                   
REMARK 500 12 PHE A  69      -50.77   -152.68                                   
REMARK 500 12 ARG A  73      -39.06   -151.58                                   
REMARK 500 12 LEU A  74      -45.67     67.84                                   
REMARK 500 12 SER A  75        5.95     83.05                                   
REMARK 500 13 SER A   4      124.51     79.20                                   
REMARK 500 13 PHE A  69      -48.14   -149.11                                   
REMARK 500 13 ALA A  77       48.30    -84.44                                   
REMARK 500 14 SER A   4      146.65     82.59                                   
REMARK 500 14 HIS A  53       -1.93     80.38                                   
REMARK 500 14 PHE A  69      -46.39   -158.69                                   
REMARK 500 14 ARG A  73      138.73     89.24                                   
REMARK 500 15 SER A   4      121.79     82.76                                   
REMARK 500 15 HIS A  53       -0.66     79.56                                   
REMARK 500 15 PHE A  69      -44.27   -156.02                                   
REMARK 500 15 ARG A  73      135.32    175.92                                   
REMARK 500 16 ASN A  37      163.84     72.75                                   
REMARK 500 16 HIS A  53       42.45     80.31                                   
REMARK 500 16 PHE A  69      -59.76   -148.49                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      60 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  2KEB A    1    78  UNP    Q14181   DPOA2_HUMAN      1     78             
SEQADV 2KEB MET A  -22  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLY A  -21  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB SER A  -20  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB SER A  -19  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -18  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -17  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -16  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -15  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -14  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB HIS A  -13  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLY A  -12  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB SER A  -11  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB SER A  -10  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB LEU A   -9  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLU A   -8  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB VAL A   -7  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB LEU A   -6  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB PHE A   -5  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLN A   -4  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLY A   -3  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB PRO A   -2  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB GLY A   -1  UNP  Q14181              EXPRESSION TAG                 
SEQADV 2KEB SER A    0  UNP  Q14181              EXPRESSION TAG                 
SEQRES   1 A  101  MET GLY SER SER HIS HIS HIS HIS HIS HIS GLY SER SER          
SEQRES   2 A  101  LEU GLU VAL LEU PHE GLN GLY PRO GLY SER MET SER ALA          
SEQRES   3 A  101  SER ALA GLN GLN LEU ALA GLU GLU LEU GLN ILE PHE GLY          
SEQRES   4 A  101  LEU ASP CYS GLU GLU ALA LEU ILE GLU LYS LEU VAL GLU          
SEQRES   5 A  101  LEU CYS VAL GLN TYR GLY GLN ASN GLU GLU GLY MET VAL          
SEQRES   6 A  101  GLY GLU LEU ILE ALA PHE CYS THR SER THR HIS LYS VAL          
SEQRES   7 A  101  GLY LEU THR SER GLU ILE LEU ASN SER PHE GLU HIS GLU          
SEQRES   8 A  101  PHE LEU SER LYS ARG LEU SER LYS ALA ARG                      
HELIX    1   1 SER A    4  GLY A   16  1                                  13    
HELIX    2   2 GLU A   20  GLY A   35  1                                  16    
HELIX    3   3 ASN A   37  HIS A   53  1                                  17    
HELIX    4   4 THR A   58  PHE A   69  1                                  12    
HELIX    5   5 PHE A   69  LEU A   74  1                                   6    
CISPEP   1 MET A    1    SER A    2         10        -0.85                     
CISPEP   2 SER A    2    ALA A    3         19        -3.00                     
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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