PDB Short entry for 1VA1
HEADER    TRANSCRIPTION                           07-FEB-04   1VA1              
TITLE     SOLUTION STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING            
TITLE    2 DOMAIN (ZINC FINGER 1)                                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TRANSCRIPTION FACTOR SP1;                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: ZINC FINGER 1;                                             
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: SP1;                                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;                            
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PEVSP1                                    
KEYWDS    C2H2 TYPE ZINC FINGER, TRANSCRIPTION FACTOR, DNA-BINDING              
KEYWDS   2 PROTEIN                                                              
EXPDTA    SOLUTION NMR                                                          
NUMMDL    31                                                                    
MDLTYP    MINIMIZED AVERAGE                                                     
AUTHOR    S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI            
REVDAT   2   24-FEB-09 1VA1    1       VERSN                                    
REVDAT   1   08-FEB-05 1VA1    0                                                
JRNL        AUTH   S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,              
JRNL        AUTH 2 Y.KOBAYASHI                                                  
JRNL        TITL   NMR STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA                
JRNL        TITL 2 BINDING DOMAIN                                               
JRNL        REF    BIOCHEMISTRY                  V.  43 16027 2004              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   15609997                                                     
JRNL        DOI    10.1021/BI048438P                                            
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.1                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3                 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,        
REMARK   3                 RICE,SIMONSON,WARREN                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1VA1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-04.                  
REMARK 100 THE RCSB ID CODE IS RCSB006394.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 7.4                                
REMARK 210  IONIC STRENGTH                 : 10MM TRIS-D, 50MM NACL             
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 1MM SP1 DNA-BINDING DOMAIN U-      
REMARK 210                                   15N/13C; 10MM TRIS-D; 50MM         
REMARK 210                                   NACL; 1MM DTT                      
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_        
REMARK 210                                   15N-SEPARATED_NOESY                
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : INOVA                              
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : CNS 1.1, NMRPIPE 2.1, NMRVIEW      
REMARK 210                                   5.0.4                              
REMARK 210   METHOD USED                   : TORSION ANGLE DYNAMICS,            
REMARK 210                                   SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 31                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 31                  
REMARK 210                                                                      
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR      
REMARK 210  SPECTROSCOPY.                                                       
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 CYS A 539       96.25    -66.11                                   
REMARK 500  2 LYS A 535      158.22     60.64                                   
REMARK 500  2 HIS A 540       30.55    -97.61                                   
REMARK 500  2 GLN A 542       83.07    -62.58                                   
REMARK 500  2 LYS A 546     -164.98   -100.10                                   
REMARK 500  2 THR A 562       36.33    -97.31                                   
REMARK 500  3 GLN A 536     -178.65     60.07                                   
REMARK 500  3 CYS A 539       91.43    -65.31                                   
REMARK 500  3 GLU A 564      -48.35   -146.58                                   
REMARK 500  4 PRO A 531       98.74    -50.90                                   
REMARK 500  4 HIS A 540       51.03   -115.96                                   
REMARK 500  4 CYS A 544     -174.97    -68.75                                   
REMARK 500  5 CYS A 544     -168.94   -107.79                                   
REMARK 500  5 THR A 562       30.62    -97.78                                   
REMARK 500  5 GLU A 564      -79.32     63.02                                   
REMARK 500  6 LYS A 535      157.37     62.53                                   
REMARK 500  6 GLN A 536      126.04     63.26                                   
REMARK 500  6 HIS A 540       33.87    -96.80                                   
REMARK 500  6 GLU A 564      -47.35   -146.24                                   
REMARK 500  7 LYS A 535     -178.53     60.07                                   
REMARK 500  7 CYS A 539       86.29    -59.91                                   
REMARK 500  8 CYS A 539       97.02    -68.90                                   
REMARK 500  9 LYS A 546     -172.42    -67.92                                   
REMARK 500 10 LYS A 535       92.25     43.48                                   
REMARK 500 11 LYS A 535      158.22     60.64                                   
REMARK 500 11 HIS A 540       30.55    -97.61                                   
REMARK 500 11 GLN A 542       83.07    -62.58                                   
REMARK 500 11 LYS A 546     -164.98   -100.10                                   
REMARK 500 11 THR A 562       36.33    -97.31                                   
REMARK 500 12 GLN A 542       89.35    -58.89                                   
REMARK 500 12 VAL A 547       87.00     57.12                                   
REMARK 500 12 GLU A 564       32.32   -161.58                                   
REMARK 500 13 GLN A 536      131.02   -172.91                                   
REMARK 500 13 CYS A 539       98.49    -62.14                                   
REMARK 500 13 CYS A 544     -165.72   -115.79                                   
REMARK 500 13 VAL A 547       86.53     53.71                                   
REMARK 500 14 HIS A 540       35.96    -96.65                                   
REMARK 500 15 CYS A 539       93.15    -64.04                                   
REMARK 500 15 CYS A 544     -168.16   -110.70                                   
REMARK 500 15 LYS A 546     -171.45    -60.76                                   
REMARK 500 15 THR A 562     -178.28     56.06                                   
REMARK 500 16 ASP A 530       98.91     60.60                                   
REMARK 500 16 CYS A 544     -165.16   -119.08                                   
REMARK 500 17 CYS A 544     -167.03    -64.91                                   
REMARK 500 17 VAL A 547       82.96     54.17                                   
REMARK 500 17 GLU A 564      165.14     60.11                                   
REMARK 500 18 PRO A 531      108.32    -51.87                                   
REMARK 500 18 GLU A 564      -45.95   -155.83                                   
REMARK 500 19 CYS A 544     -166.01    -64.98                                   
REMARK 500 19 VAL A 547       99.31     57.04                                   
REMARK 500 20 HIS A 540       40.87    -95.88                                   
REMARK 500 20 GLN A 542      -80.93     62.23                                   
REMARK 500 20 CYS A 544     -166.88    -62.67                                   
REMARK 500 20 GLU A 564      -49.86   -137.36                                   
REMARK 500 21 LYS A 535      169.66     58.27                                   
REMARK 500 21 HIS A 540       30.41    -95.04                                   
REMARK 500 21 GLN A 542       84.63    -62.02                                   
REMARK 500 21 THR A 562      -83.38     56.67                                   
REMARK 500 21 GLU A 564       98.52     60.07                                   
REMARK 500 22 GLN A 542       36.52    -92.14                                   
REMARK 500 22 CYS A 544     -169.82   -111.06                                   
REMARK 500 22 THR A 562      -85.25     55.00                                   
REMARK 500 22 GLU A 564      173.67     60.51                                   
REMARK 500 23 VAL A 547       88.91     48.35                                   
REMARK 500 24 HIS A 540       32.92    -97.57                                   
REMARK 500 24 GLN A 542      -83.68     59.47                                   
REMARK 500 24 CYS A 544     -169.05    -64.01                                   
REMARK 500 24 VAL A 547       96.23     49.76                                   
REMARK 500 25 LYS A 535      171.74     60.36                                   
REMARK 500 26 ASP A 530       93.42     60.60                                   
REMARK 500 26 PRO A 531      171.62    -50.27                                   
REMARK 500 26 GLU A 564      -57.77   -130.50                                   
REMARK 500 28 GLN A 542       73.62    -68.00                                   
REMARK 500 28 THR A 562     -172.17     52.68                                   
REMARK 500 28 GLU A 564      131.93     63.83                                   
REMARK 500 29 LYS A 535      103.15     60.24                                   
REMARK 500 29 CYS A 539       99.53    -69.69                                   
REMARK 500 29 GLN A 542       92.41    -59.73                                   
REMARK 500 29 THR A 562      172.74     50.99                                   
REMARK 500 30 GLN A 536      164.39     59.93                                   
REMARK 500 30 CYS A 539       94.54    -64.19                                   
REMARK 500 30 CYS A 544     -167.13   -112.94                                   
REMARK 500 31 PRO A 531     -177.81    -51.06                                   
REMARK 500 31 LYS A 535     -108.58    -57.36                                   
REMARK 500 31 GLN A 536      113.25     85.40                                   
REMARK 500 31 CYS A 539      101.45    -52.94                                   
REMARK 500 31 CYS A 544     -167.70    -67.07                                   
REMARK 500 31 THR A 562      100.36    -59.05                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;              
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                            
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A 100  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 539   SG                                                     
REMARK 620 2 CYS A 544   SG  121.8                                              
REMARK 620 3 HIS A 557   NE2  89.5 129.2                                        
REMARK 620 4 HIS A 561   NE2  88.9 120.9  95.9                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 100                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1VA2   RELATED DB: PDB                                   
REMARK 900 THE SAME PROTEIN, ZINC FINGER 2 DOMAIN                               
REMARK 900 RELATED ID: 1VA3   RELATED DB: PDB                                   
REMARK 900 THE SAME PROTEIN, ZINC FINGER 3 DOMAIN                               
DBREF  1VA1 A  530   565  UNP    P08047   SP1_HUMAN      619    654             
SEQADV 1VA1 MET A    1  UNP  P08047              INITIATING METHIONINE          
SEQRES   1 A   37  MET ASP PRO GLY LYS LYS LYS GLN HIS ILE CYS HIS ILE          
SEQRES   2 A   37  GLN GLY CYS GLY LYS VAL TYR GLY LYS THR SER HIS LEU          
SEQRES   3 A   37  ARG ALA HIS LEU ARG TRP HIS THR GLY GLU ARG                  
HET     ZN  A 100       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    ZN 2+                                                        
HELIX    1   1 LYS A  550  GLY A  563  1                                  14    
SHEET    1   A 2 HIS A 537  ILE A 538  0                                        
SHEET    2   A 2 VAL A 547  TYR A 548 -1  O  TYR A 548   N  HIS A 537           
LINK        ZN    ZN A 100                 SG  CYS A 539     1555   1555  2.30  
LINK        ZN    ZN A 100                 SG  CYS A 544     1555   1555  2.31  
LINK        ZN    ZN A 100                 NE2 HIS A 557     1555   1555  2.01  
LINK        ZN    ZN A 100                 NE2 HIS A 561     1555   1555  2.02  
SITE     1 AC1  4 CYS A 539  CYS A 544  HIS A 557  HIS A 561                    
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