HEADER OXIDOREDUCTASE 07-AUG-18 6HAC TITLE CRYSTAL STRUCTURE OF [FE]-HYDROGENASE (HMD) HOLOENZYME FROM TITLE 2 METHANOCOCCUS AEOLICUS (OPEN FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H(2)-DEPENDENT METHYLENE-H(4)MPT DEHYDROGENASE,H(2)-FORMING COMPND 5 N(5),N(10)-METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE,N(5),N(10)- COMPND 6 METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; COMPND 7 EC: 1.12.98.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS AEOLICUS (STRAIN ATCC BAA-1280 / SOURCE 3 DSM 17508 / OCM 812 / NANKAI-3); SOURCE 4 ORGANISM_TAXID: 419665; SOURCE 5 VARIANT: /; SOURCE 6 CELL_LINE: /; SOURCE 7 ATCC: /; SOURCE 8 ORGAN: /; SOURCE 9 TISSUE: /; SOURCE 10 CELL: /; SOURCE 11 GENE: HMD, MAEO_1025; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_VARIANT: /; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: /; SOURCE 16 EXPRESSION_SYSTEM_ATCC_NUMBER: /; SOURCE 17 EXPRESSION_SYSTEM_ORGAN: /; SOURCE 18 EXPRESSION_SYSTEM_TISSUE: /; SOURCE 19 EXPRESSION_SYSTEM_CELL: /; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET-24B+ KEYWDS [FE]-HYDROGENASE, CATALYTIC CYCLE, CONFORMATIONAL REARRANGEMENT, FE- KEYWDS 2 GUANYLYLPYRIDINOL COFACTOR, METHANOGENESIS, HYDRIDE-TRANSFER, KEYWDS 3 TETRAHYDROMETHANOPTERIN, C1-METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.HUANG,T.WAGNER,M.D.WODRICH,K.ATAKA,E.BILL,U.ERMLER,X.HU,S.SHIMA REVDAT 3 17-JAN-24 6HAC 1 REMARK REVDAT 2 04-SEP-19 6HAC 1 JRNL REVDAT 1 28-AUG-19 6HAC 0 JRNL AUTH G.HUANG,T.WAGNER,M.D.WODRICH,K.ATAKA,E.BILL,U.ERMLER,X.HU, JRNL AUTH 2 S.SHIMA JRNL TITL THE ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF ACTIVATED JRNL TITL 2 [FE]-HYDROGENASE JRNL REF NAT CATAL 2019 JRNL REFN ESSN 2520-1158 JRNL DOI 10.1038/S41929-019-0289-4 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25043 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1229 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 13 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.39 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2795 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2260 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2651 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE : 0.2634 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.15 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.59330 REMARK 3 B22 (A**2) : 2.59330 REMARK 3 B33 (A**2) : -5.18660 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.270 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.177 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.146 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.351 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.146 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5343 ; 5.000 ; HARMONIC REMARK 3 BOND ANGLES : 9741 ; 5.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1197 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 815 ; 20.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5343 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 6 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 367 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6166 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.11 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.27 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 13.75 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -2.1917 -41.5428 -22.9285 REMARK 3 T TENSOR REMARK 3 T11: -0.1389 T22: -0.1328 REMARK 3 T33: 0.1276 T12: -0.0280 REMARK 3 T13: -0.0291 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 0.3834 L22: 0.9126 REMARK 3 L33: 1.0151 L12: 0.1552 REMARK 3 L13: -0.0942 L23: -0.5705 REMARK 3 S TENSOR REMARK 3 S11: 0.0442 S12: -0.0642 S13: 0.0607 REMARK 3 S21: 0.1333 S22: -0.1338 S23: -0.1215 REMARK 3 S31: -0.1161 S32: 0.0397 S33: 0.0896 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : / REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25078 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 1.02300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 4JJF REMARK 200 REMARK 200 REMARK: TRANSPARENT DIAMOND SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE RECONSTITUTED [FE]-HYDROGENASE REMARK 280 HOLOENZYME FROM M. AEOLICUS WAS CRYSTALLIZED IN THE ANAEROBIC REMARK 280 TENT WITH GAS PHASE 95%N2/5%H2 USING 96-WELL 2-DROP MRC REMARK 280 CRYSTALLIZATION PLATES (MOLECULAR DIMENSIONS, SUFFOLK, UK). FOR REMARK 280 THE INITIAL SCREENING, 0.7-UL OF 24 MG/ML RECONSTITUTED [FE]- REMARK 280 HYDROGENASE WAS MIXED WITH 0.7 UL OF RESERVOIR SOLUTION OF REMARK 280 CRYSTALLIZATION KITS UNDER YELLOW LIGHT AND INCUBATED UNDER THE REMARK 280 DARK CONDITION. THE BEST DIFFRACTING CRYSTAL WAS OBTAINED IN ONE REMARK 280 MONTH IN THE CRYSTALLIZATION RESERVOIR SOLUTION CONTAINING 20% W/ REMARK 280 V POLYETHYLENE GLYCOL 3350, 100-MM TRI-SODIUM CITRATE PH 4.0 AND REMARK 280 200-MM TRI-SODIUM CITRATE., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 281.15K 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 68.49250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 68.49250 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.65850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.32925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 68.49250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.98775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.98775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.49250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.32925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 68.49250 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.65850 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 68.49250 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 68.49250 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 58.65850 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 68.49250 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 87.98775 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 29.32925 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 68.49250 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 29.32925 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 87.98775 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 68.49250 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 68.49250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 58.65850 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: 9550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -68.49250 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -87.98775 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 -135.29 50.79 REMARK 500 ALA A 175 -159.83 -102.68 REMARK 500 CYS A 204 178.67 174.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 402 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 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 FE9 A 401 N1 87.2 REMARK 620 3 FE9 A 401 C1F 170.8 91.5 REMARK 620 4 FE9 A 401 C8 75.8 82.8 95.0 REMARK 620 5 FE9 A 401 C2F 92.8 173.5 87.5 90.9 REMARK 620 6 HOH A 542 O 83.9 97.9 105.3 159.7 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 325 O REMARK 620 2 HOH A 605 O 107.3 REMARK 620 N 1 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 1PE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 DBREF 6HAC A 1 342 UNP A6UVT1 A6UVT1_META3 1 342 SEQRES 1 A 342 MET LYS VAL ALA ILE LEU GLY ALA GLY CYS TYR ARG SER SEQRES 2 A 342 HIS ALA ALA CYS GLY ILE THR ASN PHE SER ARG ALA ALA SEQRES 3 A 342 GLU VAL ALA ASN LYS VAL GLY ILE PRO GLU ILE THR MET SEQRES 4 A 342 THR HIS SER THR ILE THR MET GLY ALA GLU LEU LEU HIS SEQRES 5 A 342 LEU VAL ASP GLU ILE ASP GLU VAL VAL VAL SER ASP PRO SEQRES 6 A 342 CYS PHE ALA GLU GLU PRO GLY LEU ILE ILE ILE ASP GLU SEQRES 7 A 342 PHE ASP CYS LYS GLU VAL MET GLU ALA HIS LEU ALA GLY SEQRES 8 A 342 LYS ALA GLU ASP VAL MET PRO ALA ILE ARG ASP ALA VAL SEQRES 9 A 342 LYS ALA LYS ALA LYS ASP SER PRO LYS PRO PRO LYS GLY SEQRES 10 A 342 CYS ILE HIS PHE VAL ASN PRO GLU LYS VAL GLY LEU LYS SEQRES 11 A 342 VAL THR SER ASP ASP ARG GLU ALA ILE GLU GLY ALA ASP SEQRES 12 A 342 ILE VAL ILE THR TRP LEU PRO LYS GLY GLY SER GLN PRO SEQRES 13 A 342 ALA ILE ILE GLU LYS PHE VAL ASP ALA ILE LYS GLU GLY SEQRES 14 A 342 ALA ILE VAL THR HIS ALA CYS THR ILE PRO THR PRO LYS SEQRES 15 A 342 PHE ALA LYS ILE PHE LYS ASP LEU GLY ARG GLU ASP LEU SEQRES 16 A 342 ASN ILE VAL SER PHE HIS PRO GLY CYS VAL PRO GLU MET SEQRES 17 A 342 LYS GLY GLN VAL TYR LEU SER GLU GLY TYR ALA SER GLU SEQRES 18 A 342 GLU ALA VAL GLU LYS LEU TYR LYS ILE ALA LYS ILE SER SEQRES 19 A 342 ARG GLY THR ALA PHE LYS MET PRO ALA ASN LEU ILE SER SEQRES 20 A 342 PRO VAL CYS ASP MET GLY SER ALA VAL THR ALA PRO VAL SEQRES 21 A 342 TYR ALA ALA ILE LEU SER TYR ARG ASP ALA VAL THR ASN SEQRES 22 A 342 ILE LEU GLY ALA PRO ALA ASP PHE ALA GLN MET MET ALA SEQRES 23 A 342 ASP GLU ALA ILE THR GLN MET LEU GLU LEU MET ARG ASN SEQRES 24 A 342 GLU GLY ILE GLN ASN MET GLU ASN LYS LEU ASN PRO GLY SEQRES 25 A 342 ALA LEU THR GLY THR ALA ASP SER MET CYS PHE GLY PRO SEQRES 26 A 342 LEU SER GLU LEU LEU PRO ALA SER LEU LYS VAL LEU GLU SEQRES 27 A 342 GLU HIS LYS LYS HET FE9 A 401 41 HET 1PE A 402 12 HET GOL A 403 6 HET GOL A 404 6 HET NA A 405 1 HETNAM FE9 IRON-GUANYLYL PYRIDINOL COFACTOR HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN 1PE PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FE9 C21 H23 FE N6 O13 P S 4+ FORMUL 3 1PE C10 H22 O6 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 NA NA 1+ FORMUL 7 HOH *107(H2 O) HELIX 1 AA1 TYR A 11 CYS A 17 1 7 HELIX 2 AA2 PHE A 22 GLY A 33 1 12 HELIX 3 AA3 ILE A 34 THR A 40 5 7 HELIX 4 AA4 HIS A 41 VAL A 54 1 14 HELIX 5 AA5 PRO A 65 GLU A 69 5 5 HELIX 6 AA6 ASP A 80 ALA A 90 1 11 HELIX 7 AA7 LYS A 92 ASP A 95 5 4 HELIX 8 AA8 VAL A 96 SER A 111 1 16 HELIX 9 AA9 ASN A 123 GLY A 128 5 6 HELIX 10 AB1 ASP A 134 GLU A 140 1 7 HELIX 11 AB2 SER A 154 LYS A 161 1 8 HELIX 12 AB3 PHE A 162 ILE A 166 5 5 HELIX 13 AB4 PRO A 179 LEU A 190 1 12 HELIX 14 AB5 SER A 220 GLY A 236 1 17 HELIX 15 AB6 LEU A 245 ASP A 251 1 7 HELIX 16 AB7 GLY A 253 ILE A 274 1 22 HELIX 17 AB8 PRO A 278 GLY A 301 1 24 HELIX 18 AB9 ASN A 304 LEU A 309 1 6 HELIX 19 AC1 ASN A 310 ALA A 313 5 4 HELIX 20 AC2 LEU A 314 ASP A 319 1 6 HELIX 21 AC3 SER A 320 CYS A 322 5 3 HELIX 22 AC4 PHE A 323 SER A 327 5 5 HELIX 23 AC5 GLU A 328 HIS A 340 1 13 SHEET 1 AA1 6 LYS A 130 THR A 132 0 SHEET 2 AA1 6 GLU A 59 SER A 63 1 N VAL A 62 O LYS A 130 SHEET 3 AA1 6 LYS A 2 LEU A 6 1 N ILE A 5 O SER A 63 SHEET 4 AA1 6 ILE A 144 THR A 147 1 O ILE A 146 N ALA A 4 SHEET 5 AA1 6 ILE A 171 HIS A 174 1 O ILE A 171 N VAL A 145 SHEET 6 AA1 6 ASN A 196 SER A 199 1 O ASN A 196 N VAL A 172 SHEET 1 AA2 2 GLY A 72 ILE A 75 0 SHEET 2 AA2 2 GLY A 117 HIS A 120 1 O HIS A 120 N ILE A 74 SHEET 1 AA3 2 TYR A 213 GLU A 216 0 SHEET 2 AA3 2 PHE A 239 PRO A 242 1 O PHE A 239 N LEU A 214 LINK SG CYS A 176 FE FE9 A 401 1555 1555 2.56 LINK O PRO A 325 NA NA A 405 1555 1555 2.66 LINK FE FE9 A 401 O HOH A 542 1555 1555 2.32 LINK NA NA A 405 O HOH A 605 1555 1555 2.78 CISPEP 1 GLU A 70 PRO A 71 0 3.33 CISPEP 2 PRO A 114 PRO A 115 0 4.04 SITE 1 AC1 30 LEU A 6 GLY A 7 GLY A 9 CYS A 10 SITE 2 AC1 30 SER 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 HIS A 201 SITE 6 AC1 30 PRO A 202 GLY A 203 CYS A 204 VAL A 205 SITE 7 AC1 30 PRO A 206 HOH A 504 HOH A 517 HOH A 542 SITE 8 AC1 30 HOH A 543 HOH A 548 SITE 1 AC2 4 CYS A 17 ILE A 19 ASP A 102 SER A 320 SITE 1 AC3 4 ASP A 77 LYS A 107 ASN A 273 HOH A 560 SITE 1 AC4 3 GLU A 295 ARG A 298 HOH A 532 SITE 1 AC5 6 PRO A 325 LEU A 326 SER A 327 GLU A 328 SITE 2 AC5 6 LEU A 329 HOH A 605 CRYST1 136.985 136.985 117.317 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 0.007300 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008524 0.00000