HEADER OXIDOREDUCTASE 23-APR-09 3H65 TITLE THE CRYSTAL STRUCTURE OF C176A MUTATED [FE]-HYDROGENASE (HMD) TITLE 2 HOLOENZYME IN COMPLEX WITH METHYLENETETRAHYDROMETHANOPTERIN 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; COMPND 9 MUTATION: 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, C176A MUTANT, COMPLEX WITH KEYWDS 3 METHYLENETETRAHYDROMETHANOPTERIN, METHANOGENESIS, ONE-CARBON KEYWDS 4 METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HIROMOTO,E.WARKENTIN,S.SHIMA,U.ERMLER REVDAT 5 01-NOV-23 3H65 1 REMARK REVDAT 4 10-NOV-21 3H65 1 REMARK SEQADV REVDAT 3 01-NOV-17 3H65 1 REMARK REVDAT 2 13-JUL-11 3H65 1 VERSN REVDAT 1 01-SEP-09 3H65 0 JRNL AUTH T.HIROMOTO,E.WARKENTIN,J.MOLL,U.ERMLER,S.SHIMA JRNL TITL THE CRYSTAL STRUCTURE OF AN [FE]-HYDROGENASE-SUBSTRATE JRNL TITL 2 COMPLEX REVEALS THE FRAMEWORK FOR H2 ACTIVATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 48 6457 2009 JRNL REFN ISSN 1433-7851 JRNL PMID 19623593 JRNL DOI 10.1002/ANIE.200902695 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 21095 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1084 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1275 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2601 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 52.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : -1.29000 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): 0.217 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.295 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2813 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3835 ; 1.740 ; 2.033 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 354 ; 5.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;41.084 ;25.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 482 ;15.926 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;20.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2064 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1230 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1924 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 122 ; 0.134 ; 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): 60 ; 0.203 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.169 ; 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): 1809 ; 0.825 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2839 ; 1.243 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1159 ; 2.298 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 996 ; 3.605 ; 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): 20.7993 -1.3767 32.9763 REMARK 3 T TENSOR REMARK 3 T11: -0.0099 T22: -0.1683 REMARK 3 T33: -0.1788 T12: 0.0365 REMARK 3 T13: -0.0568 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 4.2364 L22: 2.1216 REMARK 3 L33: 2.1192 L12: 0.1028 REMARK 3 L13: -0.0749 L23: -0.1941 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: -0.2801 S13: -0.2059 REMARK 3 S21: 0.3123 S22: 0.0613 S23: -0.2394 REMARK 3 S31: 0.2997 S32: 0.0704 S33: -0.0427 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 244 REMARK 3 ORIGIN FOR THE GROUP (A): 32.7178 6.6687 20.0441 REMARK 3 T TENSOR REMARK 3 T11: -0.1248 T22: -0.0946 REMARK 3 T33: -0.0104 T12: 0.0665 REMARK 3 T13: -0.0015 T23: -0.0493 REMARK 3 L TENSOR REMARK 3 L11: 2.3021 L22: 3.3279 REMARK 3 L33: 2.0044 L12: 0.8816 REMARK 3 L13: 0.1090 L23: -0.3826 REMARK 3 S TENSOR REMARK 3 S11: -0.0805 S12: 0.1614 S13: -0.0203 REMARK 3 S21: -0.0435 S22: 0.0668 S23: -0.6750 REMARK 3 S31: 0.1700 S32: 0.4005 S33: 0.0137 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 245 A 327 REMARK 3 ORIGIN FOR THE GROUP (A): 13.6500 14.4199 -4.0444 REMARK 3 T TENSOR REMARK 3 T11: -0.0728 T22: -0.0544 REMARK 3 T33: -0.1701 T12: -0.0533 REMARK 3 T13: 0.0454 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 2.2841 L22: 1.4083 REMARK 3 L33: 1.4446 L12: -0.9111 REMARK 3 L13: 1.3687 L23: -1.2351 REMARK 3 S TENSOR REMARK 3 S11: 0.0207 S12: 0.3089 S13: 0.0531 REMARK 3 S21: -0.1408 S22: 0.0004 S23: -0.0555 REMARK 3 S31: -0.0195 S32: 0.1128 S33: -0.0211 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 328 A 345 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1176 14.9606 -1.9170 REMARK 3 T TENSOR REMARK 3 T11: -0.0789 T22: 0.0986 REMARK 3 T33: -0.1613 T12: -0.1026 REMARK 3 T13: 0.0267 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 14.8176 L22: 20.1271 REMARK 3 L33: 8.3927 L12: -7.4715 REMARK 3 L13: -2.7010 L23: 3.5879 REMARK 3 S TENSOR REMARK 3 S11: 0.0309 S12: -0.2441 S13: -0.2632 REMARK 3 S21: 0.0924 S22: 0.1198 S23: 1.4881 REMARK 3 S31: -0.2405 S32: -0.6840 S33: -0.1507 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 3H65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-08 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) : 0.9919 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 : 21096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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: PDB ENTRY 3F46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 100MM TRIS-HCL, 100MM REMARK 280 AMMONIUM DIHYDROGEN PHOSPHATE, 1MM DTT, PH 8.5, VAPOR DIFFUSION, REMARK 280 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 48.81500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 48.81500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.87500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.43750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.81500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.31250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.31250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.81500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.43750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 48.81500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 82.87500 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 48.81500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 48.81500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 82.87500 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 48.81500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 124.31250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 41.43750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 48.81500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 41.43750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 124.31250 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 48.81500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 48.81500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.87500 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: 9600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28550 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 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 345 CD GLU A 345 OE1 0.096 REMARK 500 GLU A 345 CD GLU A 345 OE2 0.127 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 -130.19 53.37 REMARK 500 ALA A 175 -151.48 -114.55 REMARK 500 CYS A 204 179.38 173.90 REMARK 500 GLN A 211 147.23 -175.58 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 360 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I2C A 359 N1 REMARK 620 2 I2C A 359 C8 81.1 REMARK 620 3 CMO A 361 C 94.2 101.1 REMARK 620 4 CMO A 362 C 167.2 90.8 97.2 REMARK 620 5 DTV A 363 O2 96.2 165.2 93.6 89.1 REMARK 620 6 DTV A 363 S1 85.1 91.4 167.2 85.1 73.9 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 DTV A 363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H4M A 364 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F46 RELATED DB: PDB REMARK 900 THE C176A MUTATED HOLOENZYME, RECONSTITUTED WITH IRON GUANYLYL REMARK 900 PYRIDINOL COFACTOR. REMARK 900 RELATED ID: 3F47 RELATED DB: PDB REMARK 900 THE WILD-TYPE HOLOENZYME, RECONSTITUTED WITH IRON GUANYLYL REMARK 900 PYRIDINOL COFACTOR. REMARK 900 RELATED ID: 2B0J RELATED DB: PDB REMARK 900 THE WILD-TYPE APOENZYME. DBREF 3H65 A 1 358 UNP Q58194 HMD_METJA 1 358 SEQADV 3H65 ALA A 176 UNP Q58194 CYS 176 ENGINEERED MUTATION 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 ALA 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 DTV A 363 8 HET H4M A 364 54 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 DTV (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL HETNAM H4M 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN FORMUL 2 I2C C19 H23 N6 O10 P FORMUL 3 FE2 FE 2+ FORMUL 4 CMO 2(C O) FORMUL 6 DTV C4 H10 O2 S2 FORMUL 7 H4M C31 H45 N6 O16 P FORMUL 8 HOH *102(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 ASN A 304 LEU A 309 1 6 HELIX 19 19 ASP A 310 ALA A 313 5 4 HELIX 20 20 LEU A 314 ASP A 319 1 6 HELIX 21 21 SER A 320 CYS A 322 5 3 HELIX 22 22 PHE A 323 ALA A 327 5 5 HELIX 23 23 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 60 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 THR A 198 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 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 1.81 LINK FE FE2 A 360 C CMO A 362 1555 1555 1.84 LINK FE FE2 A 360 O2 DTV A 363 1555 1555 2.04 LINK FE FE2 A 360 S1 DTV A 363 1555 1555 2.31 CISPEP 1 GLU A 70 PRO A 71 0 -0.49 CISPEP 2 PRO A 114 PRO A 115 0 3.59 SITE 1 AC1 29 LEU A 6 GLY A 7 GLY A 9 CYS A 10 SITE 2 AC1 29 THR A 13 HIS A 14 SER A 63 ASP A 64 SITE 3 AC1 29 PRO A 65 PRO A 114 PRO A 115 CYS A 118 SITE 4 AC1 29 ASP A 135 TRP A 148 LEU A 149 PRO A 150 SITE 5 AC1 29 ILE A 158 ALA A 175 ALA A 176 THR A 177 SITE 6 AC1 29 PRO A 202 FE2 A 360 CMO A 361 CMO A 362 SITE 7 AC1 29 DTV A 363 HOH A 369 HOH A 398 HOH A 415 SITE 8 AC1 29 HOH A 420 SITE 1 AC2 4 I2C A 359 CMO A 361 CMO A 362 DTV A 363 SITE 1 AC3 8 TRP A 148 CYS A 204 VAL A 205 PRO A 206 SITE 2 AC3 8 I2C A 359 FE2 A 360 CMO A 362 DTV A 363 SITE 1 AC4 6 ALA A 176 CYS A 204 I2C A 359 FE2 A 360 SITE 2 AC4 6 CMO A 361 DTV A 363 SITE 1 AC5 6 THR A 13 ALA A 176 I2C A 359 FE2 A 360 SITE 2 AC5 6 CMO A 361 CMO A 362 SITE 1 AC6 17 LYS A 151 GLY A 152 CYS A 250 ASP A 251 SITE 2 AC6 17 MET A 252 SER A 254 LEU A 275 PRO A 278 SITE 3 AC6 17 ASP A 280 PHE A 281 MET A 284 THR A 317 SITE 4 AC6 17 SER A 320 MET A 321 HOH A 365 HOH A 450 SITE 5 AC6 17 HOH A 460 CRYST1 97.630 97.630 165.750 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 0.010243 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006033 0.00000