HEADER    OXIDOREDUCTASE                          08-AUG-00   1GCU              
TITLE     CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: BILIVERDIN REDUCTASE A;                                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 EC: 1.3.1.24;                                                        
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;                              
SOURCE   3 ORGANISM_COMMON: NORWAY RAT;                                         
SOURCE   4 ORGANISM_TAXID: 10116;                                               
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    BILIVERDIN, ROSSMANN FOLD, OXIDOREDUCTASE                             
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    A.KIKUCHI,S.Y.PARK,Y.SHIRO                                            
REVDAT   5   27-DEC-23 1GCU    1       REMARK                                   
REVDAT   4   11-OCT-17 1GCU    1       REMARK                                   
REVDAT   3   24-FEB-09 1GCU    1       VERSN                                    
REVDAT   2   28-JAN-03 1GCU    1       REMARK                                   
REVDAT   1   08-FEB-01 1GCU    0                                                
JRNL        AUTH   A.KIKUCHI,S.Y.PARK,H.MIYATAKE,D.SUN,M.SATO,T.YOSHIDA,Y.SHIRO 
JRNL        TITL   CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE.               
JRNL        REF    NAT.STRUCT.BIOL.              V.   8   221 2001              
JRNL        REFN                   ISSN 1072-8368                               
JRNL        PMID   11224565                                                     
JRNL        DOI    10.1038/84955                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.40 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.851                                         
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 32.70                          
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)   (%) : 98.2                           
REMARK   3   NUMBER OF REFLECTIONS             : 71120                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.219                           
REMARK   3   FREE R VALUE                     : 0.248                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : 3606                            
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           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : NULL                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
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            : 2335                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 294                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 18.30                          
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) : 0.013                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.600                           
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 1GCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-AUG-00.                  
REMARK 100 THE DEPOSITION ID IS D_1000005037.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 20-MAR-00                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 2                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SPRING-8                           
REMARK 200  BEAMLINE                       : BL44B2                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.7                                
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 : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)                       
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 379020                             
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.400                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 32.710                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL                               
REMARK 200  DATA REDUNDANCY                : 5.300                              
REMARK 200  R MERGE                    (I) : 0.07900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 6.0000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.48                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 94.3                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.40                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.32400                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         
REMARK 200 SOFTWARE USED: SHARP                                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.49                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, NA CITRATE, NA/K TARTRATE,    
REMARK 280  PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K             
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       29.34100            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       43.93300            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       35.24350            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       43.93300            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       29.34100            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       35.24350            
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 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 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     GLN A   293                                                      
REMARK 465     LYS A   294                                                      
REMARK 465     LYS A   295                                                      
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    GLU A  52       -2.32     73.24                                   
REMARK 500    SER A 234       73.93   -118.88                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1GCU A    1   295  UNP    P46844   BIEA_RAT         1    295             
SEQRES   1 A  295  MET ASP ALA GLU PRO LYS ARG LYS PHE GLY VAL VAL VAL          
SEQRES   2 A  295  VAL GLY VAL GLY ARG ALA GLY SER VAL ARG LEU ARG ASP          
SEQRES   3 A  295  LEU LYS ASP PRO ARG SER ALA ALA PHE LEU ASN LEU ILE          
SEQRES   4 A  295  GLY PHE VAL SER ARG ARG GLU LEU GLY SER LEU ASP GLU          
SEQRES   5 A  295  VAL ARG GLN ILE SER LEU GLU ASP ALA LEU ARG SER GLN          
SEQRES   6 A  295  GLU ILE ASP VAL ALA TYR ILE CYS SER GLU SER SER SER          
SEQRES   7 A  295  HIS GLU ASP TYR ILE ARG GLN PHE LEU GLN ALA GLY LYS          
SEQRES   8 A  295  HIS VAL LEU VAL GLU TYR PRO MET THR LEU SER PHE ALA          
SEQRES   9 A  295  ALA ALA GLN GLU LEU TRP GLU LEU ALA ALA GLN LYS GLY          
SEQRES  10 A  295  ARG VAL LEU HIS GLU GLU HIS VAL GLU LEU LEU MET GLU          
SEQRES  11 A  295  GLU PHE GLU PHE LEU ARG ARG GLU VAL LEU GLY LYS GLU          
SEQRES  12 A  295  LEU LEU LYS GLY SER LEU ARG PHE THR ALA SER PRO LEU          
SEQRES  13 A  295  GLU GLU GLU ARG PHE GLY PHE PRO ALA PHE SER GLY ILE          
SEQRES  14 A  295  SER ARG LEU THR TRP LEU VAL SER LEU PHE GLY GLU LEU          
SEQRES  15 A  295  SER LEU ILE SER ALA THR LEU GLU GLU ARG LYS GLU ASP          
SEQRES  16 A  295  GLN TYR MET LYS MET THR VAL GLN LEU GLU THR GLN ASN          
SEQRES  17 A  295  LYS GLY LEU LEU SER TRP ILE GLU GLU LYS GLY PRO GLY          
SEQRES  18 A  295  LEU LYS ARG ASN ARG TYR VAL ASN PHE GLN PHE THR SER          
SEQRES  19 A  295  GLY SER LEU GLU GLU VAL PRO SER VAL GLY VAL ASN LYS          
SEQRES  20 A  295  ASN ILE PHE LEU LYS ASP GLN ASP ILE PHE VAL GLN LYS          
SEQRES  21 A  295  LEU LEU ASP GLN VAL SER ALA GLU ASP LEU ALA ALA GLU          
SEQRES  22 A  295  LYS LYS ARG ILE MET HIS CYS LEU GLY LEU ALA SER ASP          
SEQRES  23 A  295  ILE GLN LYS LEU CYS HIS GLN LYS LYS                          
FORMUL   2  HOH   *294(H2 O)                                                    
HELIX    1   1 GLY A   17  LYS A   28  1                                  12    
HELIX    2   2 ASP A   29  ALA A   34  1                                   6    
HELIX    3   3 SER A   57  SER A   64  1                                   8    
HELIX    4   4 GLU A   75  SER A   77  5                                   3    
HELIX    5   5 SER A   78  ALA A   89  1                                  12    
HELIX    6   6 SER A  102  GLY A  117  1                                  16    
HELIX    7   7 HIS A  124  LEU A  128  5                                   5    
HELIX    8   8 MET A  129  LEU A  140  1                                  12    
HELIX    9   9 GLU A  157  GLY A  162  1                                   6    
HELIX   10  10 PHE A  163  GLY A  168  1                                   6    
HELIX   11  11 GLY A  168  GLY A  180  1                                  13    
HELIX   12  12 LYS A  193  GLN A  196  5                                   4    
HELIX   13  13 ASN A  248  LEU A  262  1                                  15    
HELIX   14  14 SER A  266  HIS A  292  1                                  27    
SHEET    1   A 5 LEU A  36  VAL A  42  0                                        
SHEET    2   A 5 PHE A   9  VAL A  14  1  O  PHE A   9   N  ASN A  37           
SHEET    3   A 5 VAL A  69  ILE A  72  1  N  VAL A  69   O  GLY A  10           
SHEET    4   A 5 HIS A  92  GLU A  96  1  O  HIS A  92   N  ALA A  70           
SHEET    5   A 5 LEU A 120  GLU A 123  1  O  HIS A 121   N  VAL A  95           
SHEET    1   B 2 SER A  49  LEU A  50  0                                        
SHEET    2   B 2 VAL A  53  ARG A  54 -1  N  VAL A  53   O  LEU A  50           
SHEET    1   C 6 SER A 183  ARG A 192  0                                        
SHEET    2   C 6 TYR A 197  GLU A 205 -1  O  TYR A 197   N  ARG A 192           
SHEET    3   C 6 LEU A 211  LYS A 218 -1  N  LEU A 212   O  LEU A 204           
SHEET    4   C 6 LEU A 144  ALA A 153  1  O  LEU A 145   N  LEU A 211           
SHEET    5   C 6 ASN A 225  PHE A 232 -1  O  ASN A 225   N  THR A 152           
SHEET    6   C 6 GLY A 235  LEU A 237 -1  O  GLY A 235   N  PHE A 232           
CISPEP   1 TYR A   97    PRO A   98          0        -1.37                     
CRYST1   58.682   70.487   87.866  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      0.017041  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.014187  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011381        0.00000