PDB Short entry for 1VA2
HEADER    TRANSCRIPTION                           07-FEB-04   1VA2              
TITLE     SOLUTION STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING DOMAIN     
TITLE    2 (ZINC FINGER 2)                                                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TRANSCRIPTION FACTOR SP1;                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: ZINC FINGER 2;                                             
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 PROTEIN,     
KEYWDS   2 TRANSCRIPTION                                                        
EXPDTA    SOLUTION NMR                                                          
NUMMDL    31                                                                    
MDLTYP    MINIMIZED AVERAGE                                                     
AUTHOR    S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI            
REVDAT   4   27-DEC-23 1VA2    1       REMARK                                   
REVDAT   3   02-MAR-22 1VA2    1       REMARK                                   
REVDAT   2   24-FEB-09 1VA2    1       VERSN                                    
REVDAT   1   08-FEB-05 1VA2    0                                                
JRNL        AUTH   S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI   
JRNL        TITL   NMR STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING DOMAIN 
JRNL        REF    BIOCHEMISTRY                  V.  43 16027 2004              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   15609997                                                     
JRNL        DOI    10.1021/BI048438P                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.1, CNS 1.1                                     
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE               
REMARK   3  -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,        
REMARK   3  WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,     
REMARK   3  JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS)       
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1VA2 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 DEPOSITION ID IS D_1000006395.                                   
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 NACL;  
REMARK 210                                   1MM DTT                            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY; 3D_15N     
REMARK 210                                   -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                 : NMRPIPE 2.1, NMRVIEW 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 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: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    GLU A   583     H    HIS A   587              1.54            
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 PRO A 566       46.91    -83.22                                   
REMARK 500  1 TRP A 571      103.83    -56.39                                   
REMARK 500  1 GLU A 594      -44.68   -163.35                                   
REMARK 500  2 GLU A 594      -80.25     62.29                                   
REMARK 500  3 TRP A 571       98.02    -63.86                                   
REMARK 500  3 GLU A 594       97.02     57.23                                   
REMARK 500  4 PRO A 566       49.73    -81.66                                   
REMARK 500  4 GLU A 594      -66.26    -91.58                                   
REMARK 500  5 PRO A 566       47.16    -83.84                                   
REMARK 500  5 TRP A 571     -162.74     39.45                                   
REMARK 500  5 TYR A 573       38.35   -172.84                                   
REMARK 500  6 HIS A 591      -66.99    -95.77                                   
REMARK 500  7 PRO A 566       47.30    -84.22                                   
REMARK 500  7 TRP A 571     -163.15     40.94                                   
REMARK 500  7 TYR A 573       38.78   -172.33                                   
REMARK 500  7 THR A 592      107.98     58.62                                   
REMARK 500  8 CYS A 569     -170.45    -56.83                                   
REMARK 500  8 TRP A 571      177.82    -51.08                                   
REMARK 500  9 PRO A 566       47.63    -81.70                                   
REMARK 500  9 TRP A 571      176.53    -52.45                                   
REMARK 500  9 TYR A 573       83.51   -167.42                                   
REMARK 500  9 THR A 592       98.51     53.38                                   
REMARK 500  9 GLU A 594      -74.82    -62.50                                   
REMARK 500 10 TRP A 571      172.69    -49.25                                   
REMARK 500 11 PRO A 566       47.61    -82.60                                   
REMARK 500 11 TRP A 571      171.57    -48.31                                   
REMARK 500 11 TYR A 573       82.01   -164.38                                   
REMARK 500 12 PRO A 566       43.89    -83.53                                   
REMARK 500 12 TRP A 571     -163.79     39.94                                   
REMARK 500 12 TYR A 573       35.04   -171.64                                   
REMARK 500 13 PRO A 566       47.78    -84.34                                   
REMARK 500 13 THR A 570       37.02    -94.46                                   
REMARK 500 13 TYR A 573       75.39   -162.47                                   
REMARK 500 13 GLU A 594       73.73     60.87                                   
REMARK 500 14 TRP A 571     -163.83     40.66                                   
REMARK 500 14 TYR A 573       42.81   -171.71                                   
REMARK 500 14 THR A 592     -167.72     45.41                                   
REMARK 500 15 TRP A 571     -179.75    -52.25                                   
REMARK 500 15 TYR A 573       79.55   -163.76                                   
REMARK 500 16 PRO A 566       63.78    -68.77                                   
REMARK 500 16 LYS A 576      117.72   -160.88                                   
REMARK 500 17 TRP A 571     -176.30    -54.05                                   
REMARK 500 17 TYR A 573       76.03   -158.70                                   
REMARK 500 17 GLU A 594       85.11     60.45                                   
REMARK 500 18 PRO A 566       58.27    -66.90                                   
REMARK 500 18 TRP A 571      168.91    -47.44                                   
REMARK 500 18 TYR A 573       82.72   -161.51                                   
REMARK 500 18 THR A 592       91.49     43.35                                   
REMARK 500 19 PRO A 566       60.98    -69.22                                   
REMARK 500 19 TRP A 571      167.30    -46.24                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      92 RAMACHANDRAN OUTLIERS.                        
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                              ZN A 100  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 569   SG                                                     
REMARK 620 2 CYS A 574   SG   91.5                                              
REMARK 620 3 HIS A 587   NE2 128.8 125.9                                        
REMARK 620 4 HIS A 591   NE2 124.9  86.6  94.2                                  
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: 1VA1   RELATED DB: PDB                                   
REMARK 900 THE SAME PROTEIN, ZINC FINGER 1 DOMAIN                               
REMARK 900 RELATED ID: 1VA3   RELATED DB: PDB                                   
REMARK 900 THE SAME PROTEIN, ZINC FINGER 3 DOMAIN                               
DBREF  1VA2 A  565   595  UNP    P08047   SP1_HUMAN      654    684             
SEQRES   1 A   31  ARG PRO PHE MET CYS THR TRP SER TYR CYS GLY LYS ARG          
SEQRES   2 A   31  PHE THR ARG SER ASP GLU LEU GLN ARG HIS LYS ARG THR          
SEQRES   3 A   31  HIS THR GLY GLU LYS                                          
HET     ZN  A 100       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    ZN 2+                                                        
HELIX    1   1 ARG A  580  ARG A  589  1                                  10    
SHEET    1   A 2 PHE A 567  MET A 568  0                                        
SHEET    2   A 2 ARG A 577  PHE A 578 -1  O  PHE A 578   N  PHE A 567           
LINK        ZN    ZN A 100                 SG  CYS A 569     1555   1555  2.33  
LINK        ZN    ZN A 100                 SG  CYS A 574     1555   1555  2.34  
LINK        ZN    ZN A 100                 NE2 HIS A 587     1555   1555  2.06  
LINK        ZN    ZN A 100                 NE2 HIS A 591     1555   1555  2.02  
SITE     1 AC1  4 CYS A 569  CYS A 574  HIS A 587  HIS A 591                    
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