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 4 30-AUG-23 3DAG 1 REMARK SEQADV LINK 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,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 0.182 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1097 ; 2.622 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 911 ; 4.068 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 DEPOSITION ID IS D_1000047794. 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 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 CMO A 502 C 75.7 99.8 REMARK 620 4 CMO A 504 C 168.9 93.5 93.6 REMARK 620 5 HOH A 806 O 91.4 98.7 156.5 99.6 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) FROM REMARK 900 METHANOCALDOCOCCUS JANNASCHII COCRYSTALLIZED WITH 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]-HYDROGENASE REMARK 900 HOLOENZYME (HMD) FROM METHANOCALDOCOCCUS 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 N1 FEG A 501 FE FE2 A 503 1555 1555 2.10 LINK C CMO A 502 FE FE2 A 503 1555 1555 1.80 LINK FE FE2 A 503 C CMO A 504 1555 1555 1.80 LINK FE FE2 A 503 O HOH A 806 1555 1555 2.32 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