HEADER OXIDOREDUCTASE 07-MAR-13 4JJF TITLE CRYSTAL STRUCTURE OF FE-HYDROGENASE FROM METHANOTHERMOBACTER TITLE 2 MARBURGENSIS IN COMPLEX WITH 2-NAPHTHYLISOCYANIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE, H(2)-FORMING COMPND 5 N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE, N(5), COMPND 6 N(10)-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; COMPND 7 EC: 1.12.98.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER MARBURGENSIS; SOURCE 3 ORGANISM_TAXID: 79929; SOURCE 4 STRAIN: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / MARBURG KEYWDS ALPHA-BETA FOLD, HYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.TAMURA,E.WARKENTIN,U.ERMLER,S.SHIMA REVDAT 2 18-SEP-13 4JJF 1 JRNL REVDAT 1 07-AUG-13 4JJF 0 JRNL AUTH H.TAMURA,M.SALOMONE-STAGNI,T.FUJISHIRO,E.WARKENTIN, JRNL AUTH 2 W.MEYER-KLAUCKE,U.ERMLER,S.SHIMA JRNL TITL CRYSTAL STRUCTURES OF [FE]-HYDROGENASE IN COMPLEX WITH JRNL TITL 2 INHIBITORY ISOCYANIDES: IMPLICATIONS FOR THE H2 -ACTIVATION JRNL TITL 3 SITE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 52 9656 2013 JRNL REFN ISSN 1433-7851 JRNL PMID 23873755 JRNL DOI 10.1002/ANIE.201305089 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0095 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 34050 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1808 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2514 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.17000 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): 0.262 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.669 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5502 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7448 ; 2.026 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 686 ; 5.620 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 840 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3992 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 244 REMARK 3 RESIDUE RANGE : A 401 A 405 REMARK 3 ORIGIN FOR THE GROUP (A): -10.1510 -23.0630 -18.3560 REMARK 3 T TENSOR REMARK 3 T11: 0.1524 T22: 0.0655 REMARK 3 T33: 0.1750 T12: 0.0408 REMARK 3 T13: 0.0119 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 2.9143 L22: 1.7758 REMARK 3 L33: 4.1689 L12: -0.0952 REMARK 3 L13: -1.1420 L23: -0.3887 REMARK 3 S TENSOR REMARK 3 S11: -0.0912 S12: -0.3551 S13: -0.0670 REMARK 3 S21: 0.3552 S22: 0.1402 S23: -0.0283 REMARK 3 S31: 0.1074 S32: 0.0229 S33: -0.0490 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 244 REMARK 3 RESIDUE RANGE : B 401 B 405 REMARK 3 ORIGIN FOR THE GROUP (A): -25.1360 -0.0580 -78.1230 REMARK 3 T TENSOR REMARK 3 T11: 0.2306 T22: 0.3668 REMARK 3 T33: 0.1754 T12: 0.1091 REMARK 3 T13: -0.0250 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 1.9282 L22: 2.8049 REMARK 3 L33: 5.5057 L12: 0.1580 REMARK 3 L13: 0.2526 L23: 1.3364 REMARK 3 S TENSOR REMARK 3 S11: 0.1658 S12: 0.4866 S13: 0.1135 REMARK 3 S21: -0.4735 S22: -0.1697 S23: 0.0631 REMARK 3 S31: -0.3226 S32: -0.6458 S33: 0.0039 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 245 A 344 REMARK 3 RESIDUE RANGE : B 245 B 344 REMARK 3 ORIGIN FOR THE GROUP (A): -19.6750 -12.7160 -48.1950 REMARK 3 T TENSOR REMARK 3 T11: 0.0458 T22: 0.1089 REMARK 3 T33: 0.1269 T12: -0.0666 REMARK 3 T13: 0.0142 T23: -0.0333 REMARK 3 L TENSOR REMARK 3 L11: 2.6894 L22: 3.3835 REMARK 3 L33: 2.8119 L12: -0.9619 REMARK 3 L13: 0.7885 L23: -1.4424 REMARK 3 S TENSOR REMARK 3 S11: -0.0530 S12: 0.0653 S13: -0.1131 REMARK 3 S21: -0.1203 S22: 0.0881 S23: 0.1268 REMARK 3 S31: 0.1216 S32: -0.2819 S33: -0.0351 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4JJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-13. REMARK 100 THE RCSB ID CODE IS RCSB078121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41275 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 2.870 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.77 REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3F46 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5MM TOLUENESULFONYLMETHYLISOCYANIDE, REMARK 280 0.1 M TRIS, 0.02 M MGCL2, 30%(V/V) PENTAERYTHRITOL PROPOXYLATE REMARK 280 426, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 70.59000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.75516 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.15333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 70.59000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 40.75516 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.15333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 70.59000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 40.75516 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.15333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 81.51031 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 64.30667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 81.51031 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 64.30667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 81.51031 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.30667 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: 8360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 O2 FE9 B 401 C1B N2I B 402 1.46 REMARK 500 O2 FE9 A 401 C1B N2I A 402 1.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU A 316 CA - CB - CG ANGL. DEV. = -15.2 DEGREES REMARK 500 LEU B 316 CA - CB - CG ANGL. DEV. = -15.4 DEGREES 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 -123.03 53.69 REMARK 500 ASN A 68 -131.60 -103.53 REMARK 500 ILE A 92 -33.39 -131.89 REMARK 500 TRP A 144 66.97 -151.17 REMARK 500 ALA A 171 -141.34 -124.23 REMARK 500 LYS A 193 65.15 29.63 REMARK 500 ALA A 206 168.25 167.83 REMARK 500 SER B 42 -128.00 51.77 REMARK 500 ASN B 68 -127.26 -107.40 REMARK 500 GLN B 69 66.82 -104.52 REMARK 500 ALA B 171 -146.50 -118.97 REMARK 500 LYS B 193 82.80 50.80 REMARK 500 ALA B 206 166.53 168.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 276 22.1 L L OUTSIDE RANGE 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 FE9 B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 172 SG REMARK 620 2 FE9 B 401 N1 88.4 REMARK 620 3 FE9 B 401 C1F 171.9 89.6 REMARK 620 4 FE9 B 401 C8 78.1 76.1 93.8 REMARK 620 5 FE9 B 401 C2F 92.1 177.7 89.6 101.8 REMARK 620 6 N2I B 402 C1B 100.2 71.4 86.6 147.5 110.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE9 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 172 SG REMARK 620 2 FE9 A 401 N1 86.6 REMARK 620 3 FE9 A 401 C1F 169.6 90.1 REMARK 620 4 FE9 A 401 C8 76.6 76.0 93.0 REMARK 620 5 FE9 A 401 C2F 91.7 178.0 91.3 102.6 REMARK 620 6 N2I A 402 C1B 99.1 70.3 89.1 146.2 111.1 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 FE9 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N2I A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE9 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N2I B 402 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 HOLOENZYME FROM M. JANNASCHII REMARK 900 RELATED ID: 3DAG RELATED DB: PDB REMARK 900 HOLOENZYME FROM M. JANNASCHII COCRSTALLIZED WITH CYANIDE REMARK 900 RELATED ID: 3F46 RELATED DB: PDB REMARK 900 C176A MUTATED HOLOENZYME FROM METHANOCALDOCOCCUS JANNASCHII REMARK 900 RELATED ID: 3F47 RELATED DB: PDB REMARK 900 HOLOENZYME FROM METHANOCALDOCOCCUS JANNASCHII DBREF 4JJF A 1 344 UNP P32440 HMD_METTM 1 344 DBREF 4JJF B 1 344 UNP P32440 HMD_METTM 1 344 SEQRES 1 A 344 MET LYS LEU ALA ILE LEU GLY ALA GLY CYS TYR ARG THR SEQRES 2 A 344 HIS ALA ALA SER GLY ILE THR ASN PHE SER ARG ALA CYS SEQRES 3 A 344 GLU VAL ALA GLU MET VAL GLY LYS PRO GLU ILE ALA MET SEQRES 4 A 344 THR HIS SER THR ILE THR MET GLY ALA GLU LEU LYS GLU SEQRES 5 A 344 LEU ALA GLY VAL ASP GLU VAL VAL VAL ALA ASP PRO VAL SEQRES 6 A 344 PHE ASP ASN GLN PHE THR VAL ILE ASP ASP PHE ALA TYR SEQRES 7 A 344 GLU ASP VAL ILE GLU ALA HIS LYS GLU ASP PRO GLU LYS SEQRES 8 A 344 ILE MET PRO GLN ILE ARG GLU LYS VAL ASN GLU VAL ALA SEQRES 9 A 344 LYS GLU LEU PRO LYS PRO PRO GLU GLY ALA ILE HIS PHE SEQRES 10 A 344 THR HIS PRO GLU ASP LEU GLY PHE GLU ILE THR THR ASP SEQRES 11 A 344 ASP ARG GLU ALA VAL ALA ASP ALA ASP PHE ILE MET THR SEQRES 12 A 344 TRP PHE PRO LYS GLY ASP MET GLN PRO ASP ILE ILE ASN SEQRES 13 A 344 LYS PHE ILE ASP ASP ILE LYS PRO GLY ALA ILE VAL THR SEQRES 14 A 344 HIS ALA CYS THR ILE PRO THR THR LYS PHE TYR LYS ILE SEQRES 15 A 344 PHE GLU GLN LYS HIS GLY ASP LEU VAL THR LYS PRO GLU SEQRES 16 A 344 THR LEU ASN VAL THR SER TYR HIS PRO GLY ALA VAL PRO SEQRES 17 A 344 GLU MET LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SEQRES 18 A 344 SER GLU ASP ALA ILE GLU THR LEU PHE GLU LEU GLY GLN SEQRES 19 A 344 LYS ALA ARG GLY ASN ALA TYR ARG LEU PRO ALA GLU LEU SEQRES 20 A 344 LEU GLY PRO VAL CYS ASP MET CYS SER ALA LEU THR ALA SEQRES 21 A 344 ILE THR TYR ALA GLY ILE LEU SER TYR ARG ASP SER VAL SEQRES 22 A 344 THR GLN VAL LEU GLY ALA PRO ALA SER PHE ALA GLN MET SEQRES 23 A 344 MET ALA LYS GLU SER LEU GLU GLN ILE THR ALA LEU MET SEQRES 24 A 344 GLU LYS VAL GLY ILE ASP LYS MET GLU GLU ASN LEU ASP SEQRES 25 A 344 PRO GLY ALA LEU LEU GLY THR ALA ASP SER MET ASN PHE SEQRES 26 A 344 GLY ALA SER ALA GLU ILE LEU PRO THR VAL PHE GLU ILE SEQRES 27 A 344 LEU GLU LYS ARG LYS LYS SEQRES 1 B 344 MET LYS LEU ALA ILE LEU GLY ALA GLY CYS TYR ARG THR SEQRES 2 B 344 HIS ALA ALA SER GLY ILE THR ASN PHE SER ARG ALA CYS SEQRES 3 B 344 GLU VAL ALA GLU MET VAL GLY LYS PRO GLU ILE ALA MET SEQRES 4 B 344 THR HIS SER THR ILE THR MET GLY ALA GLU LEU LYS GLU SEQRES 5 B 344 LEU ALA GLY VAL ASP GLU VAL VAL VAL ALA ASP PRO VAL SEQRES 6 B 344 PHE ASP ASN GLN PHE THR VAL ILE ASP ASP PHE ALA TYR SEQRES 7 B 344 GLU ASP VAL ILE GLU ALA HIS LYS GLU ASP PRO GLU LYS SEQRES 8 B 344 ILE MET PRO GLN ILE ARG GLU LYS VAL ASN GLU VAL ALA SEQRES 9 B 344 LYS GLU LEU PRO LYS PRO PRO GLU GLY ALA ILE HIS PHE SEQRES 10 B 344 THR HIS PRO GLU ASP LEU GLY PHE GLU ILE THR THR ASP SEQRES 11 B 344 ASP ARG GLU ALA VAL ALA ASP ALA ASP PHE ILE MET THR SEQRES 12 B 344 TRP PHE PRO LYS GLY ASP MET GLN PRO ASP ILE ILE ASN SEQRES 13 B 344 LYS PHE ILE ASP ASP ILE LYS PRO GLY ALA ILE VAL THR SEQRES 14 B 344 HIS ALA CYS THR ILE PRO THR THR LYS PHE TYR LYS ILE SEQRES 15 B 344 PHE GLU GLN LYS HIS GLY ASP LEU VAL THR LYS PRO GLU SEQRES 16 B 344 THR LEU ASN VAL THR SER TYR HIS PRO GLY ALA VAL PRO SEQRES 17 B 344 GLU MET LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SEQRES 18 B 344 SER GLU ASP ALA ILE GLU THR LEU PHE GLU LEU GLY GLN SEQRES 19 B 344 LYS ALA ARG GLY ASN ALA TYR ARG LEU PRO ALA GLU LEU SEQRES 20 B 344 LEU GLY PRO VAL CYS ASP MET CYS SER ALA LEU THR ALA SEQRES 21 B 344 ILE THR TYR ALA GLY ILE LEU SER TYR ARG ASP SER VAL SEQRES 22 B 344 THR GLN VAL LEU GLY ALA PRO ALA SER PHE ALA GLN MET SEQRES 23 B 344 MET ALA LYS GLU SER LEU GLU GLN ILE THR ALA LEU MET SEQRES 24 B 344 GLU LYS VAL GLY ILE ASP LYS MET GLU GLU ASN LEU ASP SEQRES 25 B 344 PRO GLY ALA LEU LEU GLY THR ALA ASP SER MET ASN PHE SEQRES 26 B 344 GLY ALA SER ALA GLU ILE LEU PRO THR VAL PHE GLU ILE SEQRES 27 B 344 LEU GLU LYS ARG LYS LYS HET FE9 A 401 41 HET N2I A 402 12 HET FE9 B 401 41 HET N2I B 402 12 HETNAM FE9 IRON-GUANYLYL PYRIDINOL COFACTOR HETNAM N2I N-(NAPHTHALEN-2-YL)METHANIMINE FORMUL 3 FE9 2(C21 H23 FE N6 O13 P S 4+) FORMUL 4 N2I 2(C11 H9 N) FORMUL 7 HOH *152(H2 O) HELIX 1 1 TYR A 11 SER A 17 1 7 HELIX 2 2 PHE A 22 VAL A 32 1 11 HELIX 3 3 LYS A 34 THR A 40 5 7 HELIX 4 4 HIS A 41 ALA A 54 1 14 HELIX 5 5 PRO A 64 ASN A 68 5 5 HELIX 6 6 ALA A 77 ASP A 88 1 12 HELIX 7 7 PRO A 89 LYS A 91 5 3 HELIX 8 8 ILE A 92 LEU A 107 1 16 HELIX 9 9 HIS A 119 GLY A 124 5 6 HELIX 10 10 ASP A 130 ALA A 136 1 7 HELIX 11 11 ASP A 149 LYS A 157 1 9 HELIX 12 12 PHE A 158 ILE A 162 5 5 HELIX 13 13 PRO A 175 LYS A 186 1 12 HELIX 14 14 LYS A 193 LEU A 197 5 5 HELIX 15 15 SER A 222 GLY A 238 1 17 HELIX 16 16 ALA A 245 ASP A 253 1 9 HELIX 17 17 CYS A 255 LEU A 277 1 23 HELIX 18 18 PRO A 280 GLY A 303 1 24 HELIX 19 19 ILE A 304 MET A 307 5 4 HELIX 20 20 ASP A 312 ALA A 315 5 4 HELIX 21 21 LEU A 316 ASP A 321 1 6 HELIX 22 22 SER A 322 ASN A 324 5 3 HELIX 23 23 PHE A 325 GLU A 330 5 6 HELIX 24 24 ILE A 331 LYS A 343 1 13 HELIX 25 25 TYR B 11 GLY B 18 1 8 HELIX 26 26 PHE B 22 GLY B 33 1 12 HELIX 27 27 LYS B 34 THR B 40 5 7 HELIX 28 28 HIS B 41 LEU B 53 1 13 HELIX 29 29 PRO B 64 ASN B 68 5 5 HELIX 30 30 ALA B 77 ASP B 88 1 12 HELIX 31 31 PRO B 89 LYS B 91 5 3 HELIX 32 32 ILE B 92 LEU B 107 1 16 HELIX 33 33 HIS B 119 GLY B 124 5 6 HELIX 34 34 ASP B 130 ALA B 136 1 7 HELIX 35 35 ASP B 149 ILE B 159 1 11 HELIX 36 36 ASP B 160 ILE B 162 5 3 HELIX 37 37 PRO B 175 GLN B 185 1 11 HELIX 38 38 LYS B 193 LEU B 197 5 5 HELIX 39 39 SER B 222 GLY B 238 1 17 HELIX 40 40 LEU B 247 ASP B 253 1 7 HELIX 41 41 CYS B 255 VAL B 276 1 22 HELIX 42 42 PRO B 280 GLY B 303 1 24 HELIX 43 43 LYS B 306 LEU B 311 1 6 HELIX 44 44 ASP B 312 ALA B 315 5 4 HELIX 45 45 LEU B 316 ASP B 321 1 6 HELIX 46 46 SER B 322 ASN B 324 5 3 HELIX 47 47 PHE B 325 GLU B 330 5 6 HELIX 48 48 ILE B 331 LYS B 343 1 13 SHEET 1 A 6 GLU A 126 THR A 128 0 SHEET 2 A 6 GLU A 58 ALA A 62 1 N VAL A 61 O GLU A 126 SHEET 3 A 6 LYS A 2 LEU A 6 1 N ILE A 5 O ALA A 62 SHEET 4 A 6 PHE A 140 THR A 143 1 O MET A 142 N LEU A 6 SHEET 5 A 6 ILE A 167 HIS A 170 1 O ILE A 167 N ILE A 141 SHEET 6 A 6 ASN A 198 SER A 201 1 O ASN A 198 N VAL A 168 SHEET 1 B 2 GLN A 69 VAL A 72 0 SHEET 2 B 2 GLY A 113 HIS A 116 1 O ALA A 114 N THR A 71 SHEET 1 C 2 VAL A 214 GLU A 218 0 SHEET 2 C 2 ALA A 240 PRO A 244 1 O TYR A 241 N ILE A 216 SHEET 1 D 6 GLU B 126 THR B 128 0 SHEET 2 D 6 GLU B 58 ALA B 62 1 N VAL B 61 O THR B 128 SHEET 3 D 6 LYS B 2 LEU B 6 1 N ILE B 5 O ALA B 62 SHEET 4 D 6 PHE B 140 THR B 143 1 O MET B 142 N LEU B 6 SHEET 5 D 6 ILE B 167 HIS B 170 1 O ILE B 167 N ILE B 141 SHEET 6 D 6 ASN B 198 SER B 201 1 O ASN B 198 N VAL B 168 SHEET 1 E 2 GLN B 69 VAL B 72 0 SHEET 2 E 2 GLY B 113 HIS B 116 1 O ALA B 114 N THR B 71 SHEET 1 F 2 VAL B 214 GLU B 218 0 SHEET 2 F 2 ALA B 240 PRO B 244 1 O TYR B 241 N ILE B 216 LINK SG CYS B 172 FE FE9 B 401 1555 1555 2.41 LINK SG CYS A 172 FE FE9 A 401 1555 1555 2.52 LINK FE FE9 B 401 C1B N2I B 402 1555 1555 1.92 LINK FE FE9 A 401 C1B N2I A 402 1555 1555 1.93 CISPEP 1 PRO A 110 PRO A 111 0 1.48 CISPEP 2 PRO B 110 PRO B 111 0 5.61 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 ALA A 62 ASP A 63 SITE 3 AC1 25 PRO A 64 PRO A 110 PRO A 111 ASP A 131 SITE 4 AC1 25 TRP A 144 PHE A 145 PRO A 146 ILE A 154 SITE 5 AC1 25 ALA A 171 CYS A 172 PRO A 204 ALA A 206 SITE 6 AC1 25 VAL A 207 PRO A 208 N2I A 402 HOH A 543 SITE 7 AC1 25 HOH A 546 SITE 1 AC2 4 CYS A 172 GLY A 205 CYS A 252 FE9 A 401 SITE 1 AC3 23 LEU B 6 GLY B 7 GLY B 9 CYS B 10 SITE 2 AC3 23 THR B 13 ALA B 62 ASP B 63 PRO B 64 SITE 3 AC3 23 PRO B 110 PRO B 111 ASP B 131 TRP B 144 SITE 4 AC3 23 PHE B 145 PRO B 146 ILE B 154 ALA B 171 SITE 5 AC3 23 CYS B 172 HIS B 203 PRO B 204 ALA B 206 SITE 6 AC3 23 VAL B 207 PRO B 208 N2I B 402 SITE 1 AC4 4 CYS B 172 GLY B 205 CYS B 252 FE9 B 401 CRYST1 141.180 141.180 96.460 90.00 90.00 120.00 H 3 18 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 0.007083 0.004089 0.000000 0.00000 SCALE2 0.000000 0.008179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010367 0.00000 MASTER 452 0 4 48 20 0 15 6 0 0 0 54 END