PDB Short entry for 3DAG
HEADER    OXIDOREDUCTASE                          29-MAY-08   3DAG              
TITLE     THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE HOLOENZYME (HMD) FROM       
TITLE    2 METHANOCALDOCOCCUS JANNASCHII                                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE;          
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: H(2)-FORMING N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN    
COMPND   5 DEHYDROGENASE, N(5),N(10)-METHENYLTETRAHYDROMETHANOPTERIN            
COMPND   6 HYDROGENASE, H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE;         
COMPND   7 EC: 1.12.98.2;                                                       
COMPND   8 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII;                  
SOURCE   3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII;                           
SOURCE   4 ORGANISM_TAXID: 2190;                                                
SOURCE   5 STRAIN: DSMZ2661;                                                    
SOURCE   6 GENE: HMD, MJ0784;                                                   
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   9 EXPRESSION_SYSTEM_STRAIN: B834 (DE3)(PLYSS);                         
SOURCE  10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  11 EXPRESSION_SYSTEM_PLASMID: PET24B                                    
KEYWDS    ROSSMANN FOLD, HELIX BUNDLE, METHANOGENESIS, ONE-CARBON METABOLISM,   
KEYWDS   2 OXIDOREDUCTASE                                                       
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    O.PILAK,E.WARKENTIN,S.SHIMA,R.K.THAUER,U.ERMLER                       
REVDAT   3   13-JUL-11 3DAG    1       VERSN                                    
REVDAT   2   27-JAN-09 3DAG    1       REMARK                                   
REVDAT   1   09-DEC-08 3DAG    0                                                
JRNL        AUTH   S.SHIMA,O.PILAK,S.VOGT,M.SCHICK,M.S.STAGNI,W.MEYER-KLAUCKE,  
JRNL        AUTH 2 E.WARKENTIN,R.K.THAUER,U.ERMLER                              
JRNL        TITL   THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE REVEALS THE        
JRNL        TITL 2 GEOMETRY OF THE ACTIVE SITE.                                 
JRNL        REF    SCIENCE                       V. 321   572 2008              
JRNL        REFN                   ISSN 0036-8075                               
JRNL        PMID   18653896                                                     
JRNL        DOI    10.1126/SCIENCE.1158978                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.75 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.2.0019                                      
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 95.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 35596                          
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 + TEST SET) : 0.181                           
REMARK   3   R VALUE            (WORKING SET) : 0.179                           
REMARK   3   FREE R VALUE                     : 0.220                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1886                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.75                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.79                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2095                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 80.49                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2510                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 133                          
REMARK   3   BIN FREE R VALUE                    : 0.3220                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 2591                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 42                                      
REMARK   3   SOLVENT ATOMS            : 204                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   B VALUE TYPE : LIKELY RESIDUAL                                     
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 31.60                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.80000                                              
REMARK   3    B22 (A**2) : 0.80000                                              
REMARK   3    B33 (A**2) : -1.59000                                             
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 OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.112         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.113         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.077         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.320         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.966                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.949                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2745 ; 0.016 ; 0.022       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3729 ; 1.727 ; 2.007       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   343 ; 5.246 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   101 ;38.374 ;25.743       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   492 ;13.750 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):     7 ;22.314 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   438 ; 0.200 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1994 ; 0.007 ; 0.020       
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1350 ; 0.212 ; 0.200       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  1907 ; 0.305 ; 0.200       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   193 ; 0.125 ; 0.200       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    72 ; 0.186 ; 0.200       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    18 ; 0.335 ; 0.200       
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  1787 ; 1.038 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2818 ; 1.500 ; 2.000       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1097 ; 2.622 ; 3.000       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   911 ; 4.068 ; 4.500       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS STATISTICS                                           
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
REMARK   3                                                                      
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    NUMBER OF COMPONENTS GROUP : 3                                    
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI                         
REMARK   3    RESIDUE RANGE :   A     1        A   344                          
REMARK   3    RESIDUE RANGE :   A   501        A   501                          
REMARK   3    RESIDUE RANGE :   A   812        A   912                          
REMARK   3    ORIGIN FOR THE GROUP (A):  21.0611   4.9788  19.4654              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:  -0.0964 T22:  -0.1218                                     
REMARK   3      T33:  -0.0910 T12:  -0.0059                                     
REMARK   3      T13:  -0.0132 T23:  -0.0386                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:   0.6162 L22:   0.6422                                     
REMARK   3      L33:   1.6983 L12:  -0.1436                                     
REMARK   3      L13:   0.3524 L23:  -0.4644                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:   0.0131 S12:   0.0055 S13:  -0.0140                       
REMARK   3      S21:   0.0153 S22:   0.0336 S23:  -0.0371                       
REMARK   3      S31:   0.1327 S32:   0.0550 S33:  -0.0467                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : MASK                                                 
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.20                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING   
REMARK   3  POSITIONS                                                           
REMARK   4                                                                      
REMARK   4 3DAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-08.                  
REMARK 100 THE RCSB ID CODE IS RCSB047794.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-FEB-07                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 8.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X10SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.99198                            
REMARK 200  MONOCHROMATOR                  : SI (111)                           
REMARK 200  OPTICS                         : MIRRORS                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 225 MM CCD               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XDS                                
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 35596                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700                              
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     (%) : 0.9                                
REMARK 200  DATA REDUNDANCY                : 5.300                              
REMARK 200  R MERGE                    (I) : 0.06700                            
REMARK 200  R SYM                      (I) : 0.05500                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 16.9200                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.80                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 0.7                                
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.70                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.50000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 3.000                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: EPMR                                                  
REMARK 200 STARTING MODEL: PDB ENTRY 2BOJ                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 52.17                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 0.1M TRIS/HCL, 20MM NH4H2PO4,   
REMARK 280  PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K             
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y+1/2,Z+1/2                                     
REMARK 290       3555   -Y,X+1/2,Z+1/4                                          
REMARK 290       4555   Y+1/2,-X,Z+3/4                                          
REMARK 290       5555   -X+1/2,Y,-Z+3/4                                         
REMARK 290       6555   X,-Y+1/2,-Z+1/4                                         
REMARK 290       7555   Y+1/2,X+1/2,-Z+1/2                                      
REMARK 290       8555   -Y,-X,-Z                                                
REMARK 290       9555   X+1/2,Y+1/2,Z+1/2                                       
REMARK 290      10555   -X,-Y,Z                                                 
REMARK 290      11555   -Y+1/2,X,Z+3/4                                          
REMARK 290      12555   Y,-X+1/2,Z+1/4                                          
REMARK 290      13555   -X,Y+1/2,-Z+1/4                                         
REMARK 290      14555   X+1/2,-Y,-Z+3/4                                         
REMARK 290      15555   Y,X,-Z                                                  
REMARK 290      16555   -Y+1/2,-X+1/2,-Z+1/2                                    
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       47.96500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000       47.96500            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       82.90500            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       41.45250            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       47.96500            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      124.35750            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000      124.35750            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       47.96500            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       41.45250            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000       47.96500            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       82.90500            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   9  1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY2   9  0.000000  1.000000  0.000000       47.96500            
REMARK 290   SMTRY3   9  0.000000  0.000000  1.000000       82.90500            
REMARK 290   SMTRY1  10 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2  10  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3  10  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1  11  0.000000 -1.000000  0.000000       47.96500            
REMARK 290   SMTRY2  11  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3  11  0.000000  0.000000  1.000000      124.35750            
REMARK 290   SMTRY1  12  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2  12 -1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY3  12  0.000000  0.000000  1.000000       41.45250            
REMARK 290   SMTRY1  13 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2  13  0.000000  1.000000  0.000000       47.96500            
REMARK 290   SMTRY3  13  0.000000  0.000000 -1.000000       41.45250            
REMARK 290   SMTRY1  14  1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY2  14  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3  14  0.000000  0.000000 -1.000000      124.35750            
REMARK 290   SMTRY1  15  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2  15  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3  15  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1  16  0.000000 -1.000000  0.000000       47.96500            
REMARK 290   SMTRY2  16 -1.000000  0.000000  0.000000       47.96500            
REMARK 290   SMTRY3  16  0.000000  0.000000 -1.000000       82.90500            
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: 7170 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 26720 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL                        
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 350   BIOMT1   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  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     GLU A   345                                                      
REMARK 465     GLU A   346                                                      
REMARK 465     GLY A   347                                                      
REMARK 465     LYS A   348                                                      
REMARK 465     THR A   349                                                      
REMARK 465     LYS A   350                                                      
REMARK 465     CYS A   351                                                      
REMARK 465     GLU A   352                                                      
REMARK 465     ILE A   353                                                      
REMARK 465     MET A   354                                                      
REMARK 465     SER A   355                                                      
REMARK 465     GLN A   356                                                      
REMARK 465     LYS A   357                                                      
REMARK 465     GLU A   358                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   O    HOH A   936     O    HOH A   977              1.45            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    SER A  42     -131.76     51.45                                   
REMARK 500    ALA A 175     -145.23   -119.68                                   
REMARK 500    CYS A 204     -177.71   -179.93                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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 975        DISTANCE =  5.43 ANGSTROMS                       
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                             FE2 A 503  FE                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 176   SG                                                     
REMARK 620 2 FEG A 501   N1   85.8                                              
REMARK 620 3 HOH A 806   O    91.4  98.7                                        
REMARK 620 4 CMO A 504   C   168.9  93.5  99.6                                  
REMARK 620 5 CMO A 502   C    75.7  99.8 156.5  93.6                            
REMARK 620 N                    1     2     3     4                             
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FEG A 501                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2BOJ   RELATED DB: PDB                                   
REMARK 900 APOENZYME                                                            
REMARK 900 RELATED ID: 3DAF   RELATED DB: PDB                                   
REMARK 900 THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE HOLOENZYME (HMD)           
REMARK 900 FROM METHANOCALDOCOCCUS JANNASCHII COCRYSTALLIZED WITH               
REMARK 900 CYANIDE                                                              
REMARK 900 RELATED ID: 3F46   RELATED DB: PDB                                   
REMARK 900 C176A-MUTATED HOLOENZYME                                             
REMARK 900 RELATED ID: 3F47   RELATED DB: PDB                                   
REMARK 900 RE-INTERPRETATION OF THE IRON-LIGAND STRUCTURE OF [FE]-              
REMARK 900 HYDROGENASE HOLOENZYME (HMD) FROM METHANOCALDOCOCCUS                 
REMARK 900 JANNASCHII                                                           
DBREF  3DAG A    1   358  UNP    Q58194   HMD_METJA        1    358             
SEQADV 3DAG VAL A  339  UNP  Q58194    LYS   339 CONFLICT                       
SEQRES   1 A  358  MET LYS ILE ALA ILE LEU GLY ALA GLY CYS TYR ARG THR          
SEQRES   2 A  358  HIS ALA ALA ALA GLY ILE THR ASN PHE MET ARG ALA CYS          
SEQRES   3 A  358  GLU VAL ALA LYS GLU VAL GLY LYS PRO GLU ILE ALA LEU          
SEQRES   4 A  358  THR HIS SER SER ILE THR TYR GLY ALA GLU LEU LEU HIS          
SEQRES   5 A  358  LEU VAL PRO ASP VAL LYS GLU VAL ILE VAL SER ASP PRO          
SEQRES   6 A  358  CYS PHE ALA GLU GLU PRO GLY LEU VAL VAL ILE ASP GLU          
SEQRES   7 A  358  PHE ASP PRO LYS GLU VAL MET GLU ALA HIS LEU SER GLY          
SEQRES   8 A  358  ASN PRO GLU SER ILE MET PRO LYS ILE ARG GLU VAL VAL          
SEQRES   9 A  358  LYS ALA LYS ALA LYS GLU LEU PRO LYS PRO PRO LYS ALA          
SEQRES  10 A  358  CYS ILE HIS LEU VAL HIS PRO GLU ASP VAL GLY LEU LYS          
SEQRES  11 A  358  VAL THR SER ASP ASP ARG GLU ALA VAL GLU GLY ALA ASP          
SEQRES  12 A  358  ILE VAL ILE THR TRP LEU PRO LYS GLY ASN LYS GLN PRO          
SEQRES  13 A  358  ASP ILE ILE LYS LYS PHE ALA ASP ALA ILE PRO GLU GLY          
SEQRES  14 A  358  ALA ILE VAL THR HIS ALA CYS THR ILE PRO THR THR LYS          
SEQRES  15 A  358  PHE ALA LYS ILE PHE LYS ASP LEU GLY ARG GLU ASP LEU          
SEQRES  16 A  358  ASN ILE THR SER TYR HIS PRO GLY CYS VAL PRO GLU MET          
SEQRES  17 A  358  LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU          
SEQRES  18 A  358  GLU ALA VAL ASN LYS LEU TYR GLU ILE GLY LYS ILE ALA          
SEQRES  19 A  358  ARG GLY LYS ALA PHE LYS MET PRO ALA ASN LEU ILE GLY          
SEQRES  20 A  358  PRO VAL CYS ASP MET CYS SER ALA VAL THR ALA THR VAL          
SEQRES  21 A  358  TYR ALA GLY LEU LEU ALA TYR ARG ASP ALA VAL THR LYS          
SEQRES  22 A  358  ILE LEU GLY ALA PRO ALA ASP PHE ALA GLN MET MET ALA          
SEQRES  23 A  358  ASP GLU ALA LEU THR GLN ILE HIS ASN LEU MET LYS GLU          
SEQRES  24 A  358  LYS GLY ILE ALA ASN MET GLU GLU ALA LEU ASP PRO ALA          
SEQRES  25 A  358  ALA LEU LEU GLY THR ALA ASP SER MET CYS PHE GLY PRO          
SEQRES  26 A  358  LEU ALA GLU ILE LEU PRO THR ALA LEU LYS VAL LEU GLU          
SEQRES  27 A  358  VAL HIS LYS VAL VAL GLU GLU GLU GLY LYS THR LYS CYS          
SEQRES  28 A  358  GLU ILE MET SER GLN LYS GLU                                  
HET    FE2  A 503       1                                                       
HET    FEG  A 501      37                                                       
HET    CMO  A 502       2                                                       
HET    CMO  A 504       2                                                       
HETNAM     FE2 FE (II) ION                                                      
HETNAM     FEG 5'-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-                     
HETNAM   2 FEG  DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE          
HETNAM     CMO CARBON MONOXIDE                                                  
FORMUL   2  FE2    FE 2+                                                        
FORMUL   3  FEG    C19 H23 N6 O11 P                                             
FORMUL   4  CMO    2(C O)                                                       
FORMUL   6  HOH   *204(H2 O)                                                    
HELIX    1   1 TYR A   11  GLY A   18  1                                   8    
HELIX    2   2 PHE A   22  GLY A   33  1                                  12    
HELIX    3   3 LYS A   34  THR A   40  5                                   7    
HELIX    4   4 HIS A   41  VAL A   54  1                                  14    
HELIX    5   5 PRO A   65  GLU A   69  5                                   5    
HELIX    6   6 ASP A   80  SER A   90  1                                  11    
HELIX    7   7 ASN A   92  SER A   95  5                                   4    
HELIX    8   8 ILE A   96  GLU A  110  1                                  15    
HELIX    9   9 HIS A  123  GLY A  128  5                                   6    
HELIX   10  10 ASP A  134  GLU A  140  1                                   7    
HELIX   11  11 LYS A  154  LYS A  161  1                                   8    
HELIX   12  12 PHE A  162  ILE A  166  5                                   5    
HELIX   13  13 PRO A  179  LEU A  190  1                                  12    
HELIX   14  14 SER A  220  GLY A  236  1                                  17    
HELIX   15  15 LEU A  245  ASP A  251  1                                   7    
HELIX   16  16 CYS A  253  ILE A  274  1                                  22    
HELIX   17  17 PRO A  278  GLY A  301  1                                  24    
HELIX   18  18 ILE A  302  ALA A  308  5                                   7    
HELIX   19  19 ASP A  310  CYS A  322  5                                  13    
HELIX   20  20 PHE A  323  ALA A  327  5                                   5    
HELIX   21  21 GLU A  328  HIS A  340  1                                  13    
SHEET    1   A 6 LYS A 130  THR A 132  0                                        
SHEET    2   A 6 GLU A  59  SER A  63  1  N  VAL A  62   O  LYS A 130           
SHEET    3   A 6 LYS A   2  LEU A   6  1  N  ILE A   5   O  SER A  63           
SHEET    4   A 6 ILE A 144  THR A 147  1  O  ILE A 146   N  ALA A   4           
SHEET    5   A 6 ILE A 171  HIS A 174  1  O  THR A 173   N  VAL A 145           
SHEET    6   A 6 ASN A 196  SER A 199  1  O  ASN A 196   N  VAL A 172           
SHEET    1   B 2 GLY A  72  VAL A  75  0                                        
SHEET    2   B 2 ALA A 117  HIS A 120  1  O  HIS A 120   N  VAL A  74           
SHEET    1   C 2 VAL A 212  GLU A 216  0                                        
SHEET    2   C 2 ALA A 238  PRO A 242  1  O  PHE A 239   N  ILE A 214           
LINK         SG ACYS A 176                FE   FE2 A 503     1555   1555  2.44  
LINK        FE   FE2 A 503                 N1  FEG A 501     1555   1555  2.10  
LINK        FE   FE2 A 503                 O   HOH A 806     1555   1555  2.32  
LINK        FE   FE2 A 503                 C   CMO A 504     1555   1555  1.80  
LINK        FE   FE2 A 503                 C   CMO A 502     1555   1555  1.80  
CISPEP   1 GLU A   70    PRO A   71          0        -2.85                     
CISPEP   2 PRO A  114    PRO A  115          0         2.85                     
CISPEP   3 LYS A  151    GLY A  152          0         2.78                     
SITE     1 AC1 25 LEU A   6  GLY A   7  ALA A   8  GLY A   9                    
SITE     2 AC1 25 CYS A  10  THR A  13  HIS A  14  SER A  63                    
SITE     3 AC1 25 ASP A  64  PRO A  65  PRO A 114  PRO A 115                    
SITE     4 AC1 25 CYS A 118  ASP A 135  TRP A 148  LEU A 149                    
SITE     5 AC1 25 PRO A 150  ILE A 158  ALA A 175  CYS A 176                    
SITE     6 AC1 25 THR A 177  HIS A 201  PRO A 202  CYS A 204                    
SITE     7 AC1 25 PRO A 206                                                     
CRYST1   95.930   95.930  165.810  90.00  90.00  90.00 I 41 2 2     16          
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      0.010424  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.010424  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.006031        0.00000