HEADER OXIDOREDUCTASE 31-OCT-08 3F46 TITLE THE CRYSTAL STRUCTURE OF C176A MUTATED [FE]-HYDROGENASE (HMD) TITLE 2 HOLOENZYME FROM 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; 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, METHANOGENESIS, ONE-CARBON METABOLISM, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HIROMOTO,S.VOGT,E.WARKENTIN,R.K.THAUER,S.SHIMA,U.ERMLER REVDAT 5 01-NOV-23 3F46 1 REMARK REVDAT 4 10-NOV-21 3F46 1 REMARK SEQADV REVDAT 3 25-OCT-17 3F46 1 REMARK REVDAT 2 13-JUL-11 3F46 1 VERSN REVDAT 1 10-FEB-09 3F46 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 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 28091 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1430 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1880 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.2790 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 : 49 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 40.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : 0.87000 REMARK 3 B33 (A**2) : -1.74000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.600 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2782 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3790 ; 1.599 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 360 ; 5.209 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;38.999 ;25.758 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 484 ;14.794 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;21.103 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 437 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2052 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1272 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1929 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 167 ; 0.119 ; 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): 52 ; 0.145 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.122 ; 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): 1843 ; 0.970 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2881 ; 1.326 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1089 ; 2.430 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 909 ; 3.842 ; 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): 20.6954 -1.6772 33.2029 REMARK 3 T TENSOR REMARK 3 T11: -0.0576 T22: -0.1694 REMARK 3 T33: -0.1417 T12: -0.0130 REMARK 3 T13: -0.0386 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 3.3847 L22: 1.7623 REMARK 3 L33: 2.0270 L12: 0.0180 REMARK 3 L13: 0.1085 L23: -0.0686 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.1882 S13: -0.1692 REMARK 3 S21: 0.2267 S22: -0.0076 S23: -0.0223 REMARK 3 S31: 0.2300 S32: -0.0521 S33: -0.0282 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): 32.5704 6.4263 20.2786 REMARK 3 T TENSOR REMARK 3 T11: -0.1389 T22: -0.1058 REMARK 3 T33: -0.0771 T12: 0.0153 REMARK 3 T13: -0.0180 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 2.2530 L22: 2.3432 REMARK 3 L33: 2.4601 L12: 0.6777 REMARK 3 L13: 0.4449 L23: -0.5676 REMARK 3 S TENSOR REMARK 3 S11: -0.0426 S12: 0.2321 S13: 0.0267 REMARK 3 S21: -0.0992 S22: -0.0343 S23: -0.3550 REMARK 3 S31: 0.0353 S32: 0.3618 S33: 0.0769 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 287 REMARK 3 ORIGIN FOR THE GROUP (A): 18.4854 8.8151 -3.7398 REMARK 3 T TENSOR REMARK 3 T11: -0.1070 T22: -0.1166 REMARK 3 T33: -0.1238 T12: -0.0172 REMARK 3 T13: -0.0119 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.7377 L22: 2.7503 REMARK 3 L33: 6.6143 L12: -0.1327 REMARK 3 L13: 1.3440 L23: -0.4878 REMARK 3 S TENSOR REMARK 3 S11: 0.1138 S12: 0.2898 S13: -0.0731 REMARK 3 S21: -0.3213 S22: -0.0349 S23: 0.0207 REMARK 3 S31: 0.1267 S32: 0.0284 S33: -0.0789 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 288 A 345 REMARK 3 ORIGIN FOR THE GROUP (A): 5.1134 17.9582 -3.5259 REMARK 3 T TENSOR REMARK 3 T11: -0.1007 T22: -0.0520 REMARK 3 T33: -0.1515 T12: -0.0298 REMARK 3 T13: -0.0069 T23: 0.0617 REMARK 3 L TENSOR REMARK 3 L11: 3.1971 L22: 4.2081 REMARK 3 L33: 4.4140 L12: 0.7835 REMARK 3 L13: 1.3237 L23: 0.8443 REMARK 3 S TENSOR REMARK 3 S11: 0.0047 S12: -0.0321 S13: 0.0180 REMARK 3 S21: 0.0334 S22: 0.1265 S23: 0.3062 REMARK 3 S31: 0.0465 S32: -0.4384 S33: -0.1312 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 3F46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-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 : 28094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 41.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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 (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 49% MPD, 100MM TRIS-HCL, 50MM 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 48.17500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 48.17500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.30500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.65250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.17500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 124.95750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.95750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.17500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.65250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 48.17500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 83.30500 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 48.17500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 48.17500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 83.30500 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 48.17500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 124.95750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 41.65250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 48.17500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 41.65250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 124.95750 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 48.17500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 48.17500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 83.30500 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: 8990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -120.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 517 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 520 LIES ON A SPECIAL POSITION. 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 CYS A 204 CB CYS A 204 SG 0.104 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 -134.45 54.09 REMARK 500 ALA A 175 -149.10 -113.46 REMARK 500 CYS A 204 -172.06 -171.39 REMARK 500 CYS A 204 -172.06 173.26 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 83.8 REMARK 620 3 CMO A 361 C 93.0 96.3 REMARK 620 4 CMO A 362 C 170.8 90.1 94.5 REMARK 620 5 DTV A 363 O2 91.0 174.0 87.0 94.7 REMARK 620 6 DTV A 363 S1 86.6 93.9 169.7 87.0 82.8 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B0J RELATED DB: PDB REMARK 900 THE WILD-TYPE APOENZYME. REMARK 900 RELATED ID: 3DAG RELATED DB: PDB REMARK 900 THE WILD-TYPE HOLOENZYME, RECONSTITUTED WITH IRON GUANYLYL REMARK 900 PYRIDINOL COFACTOR. REMARK 900 RELATED ID: 3DAF RELATED DB: PDB REMARK 900 THE WILD-TYPE HOLOENZYME, INHIBITED BY CYANIDE. REMARK 900 RELATED ID: 3F47 RELATED DB: PDB DBREF 3F46 A 1 358 UNP Q58194 HMD_METJA 1 358 SEQADV 3F46 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 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 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 HOH *169(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 LEU A 315 5 6 HELIX 20 20 THR A 317 CYS A 322 5 6 HELIX 21 21 PHE A 323 ALA A 327 5 5 HELIX 22 22 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 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 ILE A 171 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 TYR A 213 GLU A 216 0 SHEET 2 C 2 PHE A 239 PRO A 242 1 O PHE A 239 N ILE A 214 LINK N1 I2C A 359 FE FE2 A 360 1555 1555 1.99 LINK C8 I2C A 359 FE FE2 A 360 1555 1555 1.93 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 2.30 CISPEP 1 GLU A 70 PRO A 71 0 -0.32 CISPEP 2 PRO A 114 PRO A 115 0 4.28 SITE 1 AC1 30 LEU A 6 GLY A 7 ALA A 8 GLY A 9 SITE 2 AC1 30 CYS A 10 THR A 13 HIS A 14 SER A 63 SITE 3 AC1 30 ASP A 64 PRO A 65 PRO A 114 PRO A 115 SITE 4 AC1 30 CYS A 118 ASP A 135 TRP A 148 LEU A 149 SITE 5 AC1 30 PRO A 150 ILE A 158 ALA A 175 ALA A 176 SITE 6 AC1 30 THR A 177 PRO A 202 FE2 A 360 CMO A 361 SITE 7 AC1 30 CMO A 362 DTV A 363 HOH A 368 HOH A 376 SITE 8 AC1 30 HOH A 417 HOH A 446 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 8 THR A 13 ALA A 17 ALA A 176 I2C A 359 SITE 2 AC5 8 FE2 A 360 CMO A 361 CMO A 362 HOH A 480 CRYST1 96.350 96.350 166.610 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 0.010379 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006002 0.00000