PDB Short entry for 1B07
HEADER    SH3 DOMAIN                              17-NOV-98   1B07              
TITLE     CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR                       
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PROTEIN (PROTO-ONCOGENE CRK (CRK));                        
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: SH3 DOMAIN;                                                
COMPND   5 SYNONYM: P38, ADAPTER MOLECULE CRK;                                  
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MOL_ID: 2;                                                           
COMPND   8 MOLECULE: PROTEIN (SH3 PEPTOID INHIBITOR);                           
COMPND   9 CHAIN: C;                                                            
COMPND  10 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;                                   
SOURCE   3 ORGANISM_COMMON: HOUSE MOUSE;                                        
SOURCE   4 ORGANISM_TAXID: 10090;                                               
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: TG1;                                       
SOURCE   8 MOL_ID: 2                                                            
KEYWDS    SH3 DOMAIN, INHIBITORS, PEPTOIDS, PROTEIN-PROTEIN RECOGNITION,        
KEYWDS   2 PROLINE-RICH MOTIFS, SIGNAL TRANSDUCTION                             
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.T.NGUYEN,C.W.TURCK,F.E.COHEN,R.N.ZUCKERMANN,W.A.LIM                 
REVDAT   4   25-DEC-13 1B07    1       FORMUL HET    HETATM HETNAM              
REVDAT   4 2                   1       LINK   SITE   VERSN                      
REVDAT   3   24-FEB-09 1B07    1       VERSN                                    
REVDAT   2   22-DEC-99 1B07    4       HEADER COMPND REMARK JRNL                
REVDAT   2 2                   4       ATOM   SOURCE SEQRES                     
REVDAT   1   06-JAN-99 1B07    0                                                
JRNL        AUTH   J.T.NGUYEN,C.W.TURCK,F.E.COHEN,R.N.ZUCKERMANN,W.A.LIM        
JRNL        TITL   EXPLOITING THE BASIS OF PROLINE RECOGNITION BY SH3 AND WW    
JRNL        TITL 2 DOMAINS: DESIGN OF N-SUBSTITUTED INHIBITORS.                 
JRNL        EDIT   F.E.BLOOM                                                    
JRNL        REF    SCIENCE                       V. 282  2088 1998              
JRNL        PUBL   AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE          
JRNL        PUBL 2 WASHINGTON, D.C.                                             
JRNL        REFN                   ISSN 0036-8075                               
JRNL        PMID   9851931                                                      
JRNL        DOI    10.1126/SCIENCE.282.5396.2088                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.843                                         
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 30.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 10000000.000                   
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0010                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 92.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 2277                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
REMARK   3   R VALUE            (WORKING SET) : 0.242                           
REMARK   3   FREE R VALUE                     : 0.354                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.100                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 229                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 8                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.50                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.61                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 276                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3170                       
REMARK   3   BIN FREE R VALUE                    : 0.4840                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 9.80                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 30                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 561                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 8                                       
REMARK   3   SOLVENT ATOMS            : 46                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
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) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.006                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.140                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
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) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
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  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1B07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-99.                  
REMARK 100 THE RCSB ID CODE IS RCSB008105.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 15-APR-98                          
REMARK 200  TEMPERATURE           (KELVIN) : 123.0                              
REMARK 200  PH                             : 6.00                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL7-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.08                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
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   : 15685                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.0                               
REMARK 200  DATA REDUNDANCY                : 8.000                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.06200                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.54                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 81.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 8.00                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.07500                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: AMORE                                                 
REMARK 200 STARTING MODEL: 1CKB                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 36.31                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG4000, 0.2 M AMMONIUM ACETATE,     
REMARK 280  PH 6.0, PH 6.00                                                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43                             
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y,X,Z+3/4                                              
REMARK 290       4555   Y,-X,Z+1/4                                              
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        0.00000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       26.30000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       39.45000            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       13.15000            
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 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: DIMERIC                           
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2                           
REMARK 350 SURFACE AREA OF THE COMPLEX: 4710 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C                                  
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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     GLY A   132                                                      
REMARK 465     HIS A   192                                                      
REMARK 465     HIS A   193                                                      
REMARK 465     HIS A   194                                                      
REMARK 465     HIS A   195                                                      
REMARK 465     HIS A   196                                                      
REMARK 465     TYR C     1                                                      
REMARK 465     ARG C    12                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     GLU C   2    CG   CD   OE1  OE2                                  
REMARK 470     VAL C   3    CG1  CG2                                            
REMARK 470     GLY C   5    O                                                   
REMARK 470     ARG C  11    CG   CD   NE   CZ   NH1  NH2                        
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH A  42        DISTANCE =  5.42 ANGSTROMS                       
REMARK 525    HOH A  47        DISTANCE =  5.90 ANGSTROMS                       
REMARK 525    HOH C  60        DISTANCE =  5.36 ANGSTROMS                       
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYJ C 1005                
DBREF  1B07 A  134   190  UNP    Q64010   CRK_MOUSE      134    190             
DBREF  1B07 C    1    12  PDB    1B07     1B07             1     12             
SEQRES   1 A   65  GLY SER ALA GLU TYR VAL ARG ALA LEU PHE ASP PHE ASN          
SEQRES   2 A   65  GLY ASN ASP GLU GLU ASP LEU PRO PHE LYS LYS GLY ASP          
SEQRES   3 A   65  ILE LEU ARG ILE ARG ASP LYS PRO GLU GLU GLN TRP TRP          
SEQRES   4 A   65  ASN ALA GLU ASP SER GLU GLY LYS ARG GLY MET ILE PRO          
SEQRES   5 A   65  VAL PRO TYR VAL GLU LYS TYR HIS HIS HIS HIS HIS HIS          
SEQRES   1 C   12  TYR GLU VAL PRO GLY PRO VAL PRO PRO ARG ARG ARG              
HET    PYJ  C1005       8                                                       
HETNAM     PYJ PHENYLETHANE                                                     
FORMUL   3  PYJ    C8 H10                                                       
FORMUL   4  HOH   *46(H2 O)                                                     
HELIX    1   1 VAL A  184  TYR A  186  5                                   3    
SHEET    1   A 5 VAL A 187  LYS A 189  0                                        
SHEET    2   A 5 TYR A 136  ALA A 139 -1  N  ARG A 138   O  GLU A 188           
SHEET    3   A 5 ILE A 158  ASP A 163 -1  N  LEU A 159   O  VAL A 137           
SHEET    4   A 5 TRP A 169  GLU A 173 -1  N  GLU A 173   O  ARG A 160           
SHEET    5   A 5 ARG A 179  PRO A 183 -1  N  ILE A 182   O  TRP A 170           
LINK         CB  PYJ C1005                 N   GLY C   5     1555   1555  1.47  
SITE     1 AC1  7 ILE A 158  ARG A 160  GLU A 173  ASP A 174                    
SITE     2 AC1  7 SER A 175  PRO C   4  GLY C   5                               
CRYST1   36.800   36.800   52.600  90.00  90.00  90.00 P 43          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      0.027174  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.027174  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.019011        0.00000