HEADER OXIDOREDUCTASE 31-OCT-08 3F47 TITLE THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) HOLOENZYME 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: DSM 2661; SOURCE 6 GENE: HMD, MJ0784; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-24B(+) KEYWDS ROSSMANN FOLD, HELIX BUNDLE, COMPLEX WITH IRON GUANYLYL PYRIDINOL KEYWDS 2 COFACTOR, METHANOGENESIS, ONE-CARBON METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HIROMOTO,O.PILAK,E.WARKENTIN,R.K.THAUER,S.SHIMA,U.ERMLER REVDAT 4 01-NOV-23 3F47 1 REMARK LINK REVDAT 3 25-OCT-17 3F47 1 REMARK REVDAT 2 13-JUL-11 3F47 1 VERSN REVDAT 1 10-FEB-09 3F47 0 JRNL AUTH T.HIROMOTO,K.ATAKA,O.PILAK,S.VOGT,M.S.STAGNI, JRNL AUTH 2 W.MEYER-KLAUCKE,E.WARKENTIN,R.K.THAUER,S.SHIMA,U.ERMLER JRNL TITL THE CRYSTAL STRUCTURE OF C176A MUTATED [FE]-HYDROGENASE JRNL TITL 2 SUGGESTS AN ACYL-IRON LIGATION IN THE ACTIVE SITE IRON JRNL TITL 3 COMPLEX. JRNL REF FEBS LETT. V. 583 585 2009 JRNL REFN ISSN 0014-5793 JRNL PMID 19162018 JRNL DOI 10.1016/J.FEBSLET.2009.01.017 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.SHIMA,O.PILAK,S.VOGT,M.SCHICK,M.S.STAGNI,W.MEYER-KLAUCKE, REMARK 1 AUTH 2 E.WARKENTIN,R.K.THAUER,U.ERMLER REMARK 1 TITL THE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE REVEALS THE REMARK 1 TITL 2 GEOMETRY OF THE ACTIVE SITE REMARK 1 REF SCIENCE V. 321 572 2008 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 37574 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1887 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) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2205 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2593 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -1.65000 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): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.613 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2818 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3853 ; 1.578 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 370 ; 5.255 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.713 ;25.784 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;13.397 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;21.905 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2110 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1381 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1981 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 235 ; 0.124 ; 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): 67 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.144 ; 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): 1802 ; 0.749 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2933 ; 1.294 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1047 ; 2.474 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 920 ; 3.978 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 154 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6872 -1.6043 33.0099 REMARK 3 T TENSOR REMARK 3 T11: -0.0641 T22: -0.1625 REMARK 3 T33: -0.1500 T12: 0.0104 REMARK 3 T13: -0.0431 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 3.2611 L22: 1.4131 REMARK 3 L33: 1.9771 L12: 0.2209 REMARK 3 L13: -0.1466 L23: 0.0266 REMARK 3 S TENSOR REMARK 3 S11: 0.0277 S12: -0.2190 S13: -0.1425 REMARK 3 S21: 0.1816 S22: 0.0232 S23: 0.0095 REMARK 3 S31: 0.2777 S32: 0.0370 S33: -0.0509 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 155 A 240 REMARK 3 ORIGIN FOR THE GROUP (A): 32.6133 6.2578 20.5073 REMARK 3 T TENSOR REMARK 3 T11: -0.1533 T22: -0.1026 REMARK 3 T33: -0.1168 T12: 0.0302 REMARK 3 T13: -0.0276 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 2.5241 L22: 2.1824 REMARK 3 L33: 2.1095 L12: 0.8359 REMARK 3 L13: 0.2562 L23: -0.2206 REMARK 3 S TENSOR REMARK 3 S11: -0.0110 S12: 0.1280 S13: 0.0820 REMARK 3 S21: -0.0687 S22: 0.0133 S23: -0.2375 REMARK 3 S31: 0.0672 S32: 0.3241 S33: -0.0024 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 241 A 286 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0845 8.5403 -2.5684 REMARK 3 T TENSOR REMARK 3 T11: -0.1176 T22: -0.1351 REMARK 3 T33: -0.1443 T12: -0.0166 REMARK 3 T13: 0.0020 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 2.7778 L22: 2.0010 REMARK 3 L33: 4.6790 L12: -0.1081 REMARK 3 L13: 1.3762 L23: -0.1603 REMARK 3 S TENSOR REMARK 3 S11: 0.0836 S12: 0.2550 S13: -0.0414 REMARK 3 S21: -0.2346 S22: -0.0172 S23: -0.0301 REMARK 3 S31: 0.1142 S32: 0.1588 S33: -0.0664 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 287 A 345 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2014 17.7320 -3.6195 REMARK 3 T TENSOR REMARK 3 T11: -0.1356 T22: -0.0812 REMARK 3 T33: -0.1658 T12: -0.0318 REMARK 3 T13: -0.0075 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 2.6679 L22: 4.4697 REMARK 3 L33: 4.3531 L12: 0.3991 REMARK 3 L13: 1.0204 L23: 0.8168 REMARK 3 S TENSOR REMARK 3 S11: 0.0150 S12: -0.0122 S13: -0.0097 REMARK 3 S21: -0.0063 S22: 0.1239 S23: 0.2245 REMARK 3 S31: 0.0132 S32: -0.3498 S33: -0.1389 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: NULL REMARK 4 REMARK 4 3F47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050125. 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) : 0.9920 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 26.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.50800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: 3DAG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 100MM TRIS-HCL, 20MM AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, 1MM DTT , PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 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: 8480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 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: 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 -131.41 54.27 REMARK 500 ASN A 153 31.76 -85.72 REMARK 500 ALA A 175 -146.31 -121.07 REMARK 500 CYS A 204 -172.84 -173.08 REMARK 500 CYS A 204 175.70 173.17 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 NA A 363 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 51 O REMARK 620 2 VAL A 54 O 98.5 REMARK 620 3 VAL A 57 O 97.3 90.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 360 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 I2C A 359 N1 87.5 REMARK 620 3 I2C A 359 C8 74.3 83.7 REMARK 620 4 CMO A 361 C 171.3 91.5 97.1 REMARK 620 5 CMO A 362 C 91.2 175.1 91.4 89.0 REMARK 620 6 HOH A 364 O 91.4 95.3 165.7 97.2 89.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I2C A 359 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CMO A 362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 363 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B0J RELATED DB: PDB REMARK 900 THE HMD APOENZYME. REMARK 900 RELATED ID: 3DAG RELATED DB: PDB REMARK 900 THE HMD HOLOENZYME, RECONSTITUTED WITH IRON GUANYLYL PYRIDINOL REMARK 900 COFACTOR. REMARK 900 RELATED ID: 3DAF RELATED DB: PDB REMARK 900 THE HMD HOLOENZYME, INHIBITED BY CYANIDE. REMARK 900 RELATED ID: 3F46 RELATED DB: PDB DBREF 3F47 A 1 358 UNP Q58194 HMD_METJA 1 358 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 LYS HIS LYS VAL VAL GLU GLU GLU GLY LYS THR LYS CYS SEQRES 28 A 358 GLU ILE MET SER GLN LYS GLU HET I2C A 359 36 HET FE2 A 360 1 HET CMO A 361 2 HET CMO A 362 2 HET NA A 363 1 HETNAM I2C 5'-O-[(S)-HYDROXY{[2-HYDROXY-3,5-DIMETHYL-6-(2- HETNAM 2 I2C OXOETHYL)PYRIDIN-4-YL]OXY}PHOSPHORYL]GUANOSINE HETNAM FE2 FE (II) ION HETNAM CMO CARBON MONOXIDE HETNAM NA SODIUM ION FORMUL 2 I2C C19 H23 N6 O10 P FORMUL 3 FE2 FE 2+ FORMUL 4 CMO 2(C O) FORMUL 6 NA NA 1+ FORMUL 7 HOH *238(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 LYS A 109 1 14 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 ILE A 61 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 O LEU A 51 NA NA A 363 1555 1555 2.71 LINK O VAL A 54 NA NA A 363 1555 1555 2.66 LINK O VAL A 57 NA NA A 363 1555 1555 2.59 LINK SG CYS A 176 FE FE2 A 360 1555 1555 2.38 LINK N1 I2C A 359 FE FE2 A 360 1555 1555 2.01 LINK C8 I2C A 359 FE FE2 A 360 1555 1555 1.91 LINK FE FE2 A 360 C CMO A 361 1555 1555 1.83 LINK FE FE2 A 360 C CMO A 362 1555 1555 1.86 LINK FE FE2 A 360 O HOH A 364 1555 1555 2.33 CISPEP 1 GLU A 70 PRO A 71 0 -4.91 CISPEP 2 GLU A 70 PRO A 71 0 2.14 CISPEP 3 PRO A 114 PRO A 115 0 3.53 SITE 1 AC1 30 LEU A 6 GLY A 7 GLY A 9 CYS A 10 SITE 2 AC1 30 THR A 13 SER A 63 ASP A 64 PRO A 65 SITE 3 AC1 30 PRO A 114 PRO A 115 CYS A 118 ASP A 135 SITE 4 AC1 30 TRP A 148 LEU A 149 PRO A 150 ILE A 158 SITE 5 AC1 30 ALA A 175 CYS A 176 THR A 177 PRO A 202 SITE 6 AC1 30 FE2 A 360 CMO A 361 CMO A 362 HOH A 364 SITE 7 AC1 30 HOH A 373 HOH A 385 HOH A 404 HOH A 471 SITE 8 AC1 30 HOH A 487 HOH A 493 SITE 1 AC2 5 CYS A 176 I2C A 359 CMO A 361 CMO A 362 SITE 2 AC2 5 HOH A 364 SITE 1 AC3 7 TRP A 148 CYS A 204 VAL A 205 PRO A 206 SITE 2 AC3 7 I2C A 359 FE2 A 360 CMO A 362 SITE 1 AC4 8 CYS A 176 HIS A 201 PRO A 202 CYS A 204 SITE 2 AC4 8 I2C A 359 FE2 A 360 CMO A 361 HOH A 364 SITE 1 AC5 4 LEU A 51 VAL A 54 PRO A 55 VAL A 57 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