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Database: PDB
Entry: 1Q2Y
LinkDB: 1Q2Y
Original site: 1Q2Y 
HEADER    STRUCTURAL GENOMICS, UNKNOWN FUNCTION   27-JUL-03   1Q2Y              
TITLE     CRYSTAL STRUCTURE OF THE PROTEIN YJCF FROM BACILLUS SUBTILIS: A MEMBER
TITLE    2 OF THE GCN5-RELATED N-ACETYLTRANSFERASE SUPERFAMILY FOLD             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SIMILAR TO HYPOTHETICAL PROTEINS;                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: PROTEIN YJCF;                                               
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;                              
SOURCE   3 ORGANISM_TAXID: 1423;                                                
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    GCN5-RELATED N-ACETYLTRANSFERASE SUPERFAMILY FOLD, NYSGXRC, T804,     
KEYWDS   2 PSI, PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR  
KEYWDS   3 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS, UNKNOWN FUNCTION           
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    A.A.FEDOROV,U.A.RAMAGOPAL,E.V.FEDOROV,R.THIRUMURUHAN,S.C.ALMO,        
AUTHOR   2 S.K.BURLEY,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS      
AUTHOR   3 (NYSGXRC)                                                            
REVDAT   5   03-FEB-21 1Q2Y    1       AUTHOR                                   
REVDAT   4   24-FEB-09 1Q2Y    1       VERSN                                    
REVDAT   3   25-JAN-05 1Q2Y    1       AUTHOR KEYWDS REMARK                     
REVDAT   2   18-NOV-03 1Q2Y    1       KEYWDS HEADER                            
REVDAT   1   19-AUG-03 1Q2Y    0                                                
JRNL        AUTH   A.A.FEDOROV,U.A.RAMAGOPAL,E.V.FEDOROV,R.THIRUMURUHAN,        
JRNL        AUTH 2 S.C.ALMO                                                     
JRNL        TITL   CRYSTAL STRUCTURE OF THE PROTEIN YJCF FROM BACILLUS          
JRNL        TITL 2 SUBTILIS: A MEMBER OF THE GCN5-RELATED N-ACETYLTRANSFERASE   
JRNL        TITL 3 SUPERFAMILY                                                  
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.0                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : ENGH & HUBER                                    
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 15.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 93.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 9584                           
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) : 0.234                           
REMARK   3   FREE R VALUE                     : 0.265                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.300                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 507                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.006                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 10                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.00                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.09                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 83.00                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1170                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2420                       
REMARK   3   BIN FREE R VALUE                    : 0.2940                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.00                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 29                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.021                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1101                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 36                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 39.20                          
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) : 0.26                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.12                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.32                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.22                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.006                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.360                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.50                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.720                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : 3.260 ; 1.500                
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 5.110 ; 2.000                
REMARK   3   SIDE-CHAIN BOND              (A**2) : 5.980 ; 2.000                
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 9.300 ; 2.500                
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.41                                                 
REMARK   3   BSOL        : 57.83                                                
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  : PROTEIN_REP.PARAM                              
REMARK   3  PARAMETER FILE  2  : ION.PARAM                                      
REMARK   3  PARAMETER FILE  3  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP                                    
REMARK   3  TOPOLOGY FILE  2   : ION.TOP                                        
REMARK   3  TOPOLOGY FILE  3   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1Q2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-03.                  
REMARK 100 THE DEPOSITION ID IS D_1000019849.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 24-FEB-03                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : NSLS                               
REMARK 200  BEAMLINE                       : X9A                                
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0088                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 9584                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 15.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 93.0                               
REMARK 200  DATA REDUNDANCY                : 4.100                              
REMARK 200  R MERGE                    (I) : 0.04800                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 32.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.09                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 92.1                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.15300                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 7.800                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR                          
REMARK 200 SOFTWARE USED: SOLVE                                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 45.13                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550, AMMONIUM TARTRATE, BISTRIS ,    
REMARK 280  PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K             
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       17.63300            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       35.77800            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       29.64150            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       35.77800            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       17.63300            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       29.64150            
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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER                         
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: 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    VAL A  24      -60.31    -90.23                                   
REMARK 500    GLN A  27     -132.67    -81.27                                   
REMARK 500    ASN A  28       19.11   -153.41                                   
REMARK 500    ALA A  31      -85.58     -5.18                                   
REMARK 500    ASP A 129      -63.73    -95.53                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: NYSGXRC-T804   RELATED DB: TARGETDB                      
DBREF  1Q2Y A    1   140  UNP    O31628   O31628_BACSU     1    140             
SEQRES   1 A  140  MET LYS ALA VAL ILE ALA LYS ASN GLU GLU GLN LEU LYS          
SEQRES   2 A  140  ASP ALA PHE TYR VAL ARG GLU GLU VAL PHE VAL LYS GLU          
SEQRES   3 A  140  GLN ASN VAL PRO ALA GLU GLU GLU ILE ASP GLU LEU GLU          
SEQRES   4 A  140  ASN GLU SER GLU HIS ILE VAL VAL TYR ASP GLY GLU LYS          
SEQRES   5 A  140  PRO VAL GLY ALA GLY ARG TRP ARG MET LYS ASP GLY TYR          
SEQRES   6 A  140  GLY LYS LEU GLU ARG ILE CYS VAL LEU LYS SER HIS ARG          
SEQRES   7 A  140  SER ALA GLY VAL GLY GLY ILE ILE MET LYS ALA LEU GLU          
SEQRES   8 A  140  LYS ALA ALA ALA ASP GLY GLY ALA SER GLY PHE ILE LEU          
SEQRES   9 A  140  ASN ALA GLN THR GLN ALA VAL PRO PHE TYR LYS LYS HIS          
SEQRES  10 A  140  GLY TYR ARG VAL LEU SER GLU LYS GLU PHE LEU ASP ALA          
SEQRES  11 A  140  GLY ILE PRO HIS LEU GLN MET MET LYS ASP                      
FORMUL   2  HOH   *36(H2 O)                                                     
HELIX    1   1 ASN A    8  VAL A   24  1                                  17    
HELIX    2   2 LEU A   38  SER A   42  5                                   5    
HELIX    3   3 LEU A   74  ARG A   78  5                                   5    
HELIX    4   4 GLY A   81  GLY A   97  1                                  17    
HELIX    5   5 ALA A  110  HIS A  117  1                                   8    
SHEET    1   A 7 LYS A   2  ALA A   6  0                                        
SHEET    2   A 7 GLU A  43  ASP A  49 -1  O  TYR A  48   N  LYS A   2           
SHEET    3   A 7 LYS A  52  LYS A  62 -1  O  VAL A  54   N  VAL A  47           
SHEET    4   A 7 TYR A  65  CYS A  72 -1  O  LYS A  67   N  ARG A  60           
SHEET    5   A 7 PHE A 102  GLN A 107  1  O  ILE A 103   N  LEU A  68           
SHEET    6   A 7 PRO A 133  LYS A 139 -1  O  LYS A 139   N  PHE A 102           
SHEET    7   A 7 ARG A 120  VAL A 121 -1  N  ARG A 120   O  MET A 138           
SHEET    1   B 7 LYS A   2  ALA A   6  0                                        
SHEET    2   B 7 GLU A  43  ASP A  49 -1  O  TYR A  48   N  LYS A   2           
SHEET    3   B 7 LYS A  52  LYS A  62 -1  O  VAL A  54   N  VAL A  47           
SHEET    4   B 7 TYR A  65  CYS A  72 -1  O  LYS A  67   N  ARG A  60           
SHEET    5   B 7 PHE A 102  GLN A 107  1  O  ILE A 103   N  LEU A  68           
SHEET    6   B 7 PRO A 133  LYS A 139 -1  O  LYS A 139   N  PHE A 102           
SHEET    7   B 7 PHE A 127  LEU A 128 -1  N  PHE A 127   O  HIS A 134           
CRYST1   35.266   59.283   71.556  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      0.028356  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.016868  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.013975        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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