HEADER    OXIDOREDUCTASE                          24-JAN-08   3C1R              
TITLE     CRYSTAL STRUCTURE OF OXIDIZED GRX1                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: GLUTAREDOXIN-1;                                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 1;                     
COMPND   5 EC: 1.20.4.1;                                                        
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;                       
SOURCE   3 ORGANISM_COMMON: BAKER'S YEAST;                                      
SOURCE   4 ORGANISM_TAXID: 4932;                                                
SOURCE   5 STRAIN: S288C;                                                       
SOURCE   6 GENE: GRX1;                                                          
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE  10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  11 EXPRESSION_SYSTEM_PLASMID: PET28B                                    
KEYWDS    OXIDIZED FORM, OXIDOREDUCTASE, CYTOPLASM, ELECTRON TRANSPORT, REDOX-  
KEYWDS   2 ACTIVE CENTER, TRANSPORT                                             
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.YU,C.Z.ZHOU                                                         
REVDAT   3   16-OCT-24 3C1R    1       REMARK                                   
REVDAT   2   01-NOV-23 3C1R    1       REMARK SEQADV                            
REVDAT   1   09-DEC-08 3C1R    0                                                
JRNL        AUTH   J.YU,N.N.ZHANG,P.D.YIN,P.X.CUI,C.Z.ZHOU                      
JRNL        TITL   GLUTATHIONYLATION-TRIGGERED CONFORMATIONAL CHANGES OF        
JRNL        TITL 2 GLUTAREDOXIN GRX1 FROM THE YEAST SACCHAROMYCES CEREVISIAE.   
JRNL        REF    PROTEINS                      V.  72  1077 2008              
JRNL        REFN                   ISSN 0887-3585                               
JRNL        PMID   18473363                                                     
JRNL        DOI    10.1002/PROT.22096                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.                                       
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,              
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) : 28.11                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 616709.750                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 95.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 7126                           
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) : 0.193                           
REMARK   3   FREE R VALUE                     : 0.205                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 364                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.011                           
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) : 2.07                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 90.30                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 632                          
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2020                       
REMARK   3   BIN FREE R VALUE                    : 0.2190                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.20                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 364                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.037                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 870                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 12                                      
REMARK   3   SOLVENT ATOMS            : 117                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 8.20                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 16.20                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.00000                                              
REMARK   3    B22 (A**2) : 0.00000                                              
REMARK   3    B33 (A**2) : 0.00000                                              
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.21                            
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) : 0.24                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.12                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.009                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.300                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.60                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.490                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
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  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.36                                                 
REMARK   3   BSOL        : 37.67                                                
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  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  3  : MES_PAR.PARAM                                  
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP                                    
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  3   : MES_TOP.TOP                                    
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 3C1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-08.                  
REMARK 100 THE DEPOSITION ID IS D_1000046232.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : NULL                               
REMARK 200  TEMPERATURE           (KELVIN) : 100.0                              
REMARK 200  PH                             : 6.50                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU                             
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : YALE MIRRORS                       
REMARK 200  OPTICS                         : MIRRORS                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : MAR SCANNER 345 MM PLATE           
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : AUTOMAR                            
REMARK 200  DATA SCALING SOFTWARE          : AUTOMAR                            
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 7126                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 28.110                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.3                               
REMARK 200  DATA REDUNDANCY                : 4.050                              
REMARK 200  R MERGE                    (I) : 0.06100                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 9.6000                             
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) : 2.07                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 90.9                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.12                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.10700                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.200                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP                                                
REMARK 200 STARTING MODEL: 2FLS                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 40.41                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 20000, 0.1M MES, PH 6.50,        
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,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        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       24.81550            
REMARK 290   SMTRY3   2  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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
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 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     MET A    -7                                                      
REMARK 465     GLY A    -6                                                      
REMARK 465     HIS A    -5                                                      
REMARK 465     HIS A    -4                                                      
REMARK 465     HIS A    -3                                                      
REMARK 465     HIS A    -2                                                      
REMARK 465     HIS A    -1                                                      
REMARK 465     ASN A   110                                                      
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 3440                
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 3C1S   RELATED DB: PDB                                   
DBREF  3C1R A    1   110  UNP    P25373   GLRX1_YEAST      1    110             
SEQADV 3C1R MET A   -7  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R GLY A   -6  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A   -5  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A   -4  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A   -3  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A   -2  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A   -1  UNP  P25373              EXPRESSION TAG                 
SEQADV 3C1R HIS A    0  UNP  P25373              EXPRESSION TAG                 
SEQRES   1 A  118  MET GLY HIS HIS HIS HIS HIS HIS MET VAL SER GLN GLU          
SEQRES   2 A  118  THR ILE LYS HIS VAL LYS ASP LEU ILE ALA GLU ASN GLU          
SEQRES   3 A  118  ILE PHE VAL ALA SER LYS THR TYR CYS PRO TYR CYS HIS          
SEQRES   4 A  118  ALA ALA LEU ASN THR LEU PHE GLU LYS LEU LYS VAL PRO          
SEQRES   5 A  118  ARG SER LYS VAL LEU VAL LEU GLN LEU ASN ASP MET LYS          
SEQRES   6 A  118  GLU GLY ALA ASP ILE GLN ALA ALA LEU TYR GLU ILE ASN          
SEQRES   7 A  118  GLY GLN ARG THR VAL PRO ASN ILE TYR ILE ASN GLY LYS          
SEQRES   8 A  118  HIS ILE GLY GLY ASN ASP ASP LEU GLN GLU LEU ARG GLU          
SEQRES   9 A  118  THR GLY GLU LEU GLU GLU LEU LEU GLU PRO ILE LEU ALA          
SEQRES  10 A  118  ASN                                                          
HET    MES  A3440      12                                                       
HETNAM     MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID                             
FORMUL   2  MES    C6 H13 N O4 S                                                
FORMUL   3  HOH   *117(H2 O)                                                    
HELIX    1   1 SER A    3  ASN A   17  1                                  15    
HELIX    2   2 CYS A   27  GLU A   39  1                                  13    
HELIX    3   3 PRO A   44  SER A   46  5                                   3    
HELIX    4   4 ASN A   54  MET A   56  5                                   3    
HELIX    5   5 GLU A   58  GLY A   71  1                                  14    
HELIX    6   6 GLY A   87  THR A   97  1                                  11    
HELIX    7   7 GLY A   98  ALA A  109  1                                  12    
SHEET    1   A 4 VAL A  48  GLN A  52  0                                        
SHEET    2   A 4 ILE A  19  SER A  23  1  N  SER A  23   O  LEU A  51           
SHEET    3   A 4 ASN A  77  ILE A  80 -1  O  ASN A  77   N  ALA A  22           
SHEET    4   A 4 LYS A  83  GLY A  86 -1  O  GLY A  86   N  ILE A  78           
SSBOND   1 CYS A   27    CYS A   30                          1555   1555  2.06  
CISPEP   1 VAL A   75    PRO A   76          0         3.35                     
SITE     1 AC1 10 ALA A  15  TYR A  29  PRO A  76  ASN A  81                    
SITE     2 AC1 10 GLY A  82  GLY A  87  ASN A  88  ASP A  89                    
SITE     3 AC1 10 HOH A3461  HOH A3465                                          
CRYST1   28.210   49.631   39.701  90.00  94.95  90.00 P 1 21 1      2          
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      0.035448  0.000000  0.003070        0.00000                         
SCALE2      0.000000  0.020149  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.025283        0.00000