HEADER OXIDOREDUCTASE 14-JUN-99 1H2R TITLE THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM TITLE 2 DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT TITLE 3 1.4 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL COMPND 3 SUBUNIT); COMPND 4 CHAIN: S; COMPND 5 SYNONYM: HYDROGEN: FERRICYTOCHROME-C3 OXIDOREDUCTASE; COMPND 6 EC: 1.12.2.1; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE COMPND 9 SUBUNIT); COMPND 10 CHAIN: L; COMPND 11 SYNONYM: HYDROGEN: FERRICYTOCHROME-C3 OXIDOREDUCTASE; COMPND 12 EC: 1.12.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI SOURCE 3 F'; SOURCE 4 ORGANISM_TAXID: 883; SOURCE 5 STRAIN: MIYAZAKI F; SOURCE 6 ATCC: IAM 12604; SOURCE 7 COLLECTION: IAM 12604; SOURCE 8 CELLULAR_LOCATION: PERIPLASMIC MEMBRANE; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI SOURCE 11 F'; SOURCE 12 ORGANISM_TAXID: 883; SOURCE 13 STRAIN: MIYAZAKI F; SOURCE 14 ATCC: IAM 12604; SOURCE 15 COLLECTION: IAM 12604; SOURCE 16 CELLULAR_LOCATION: PERIPLASMIC MEMBRANE KEYWDS HIGH RESOLUTION CRYSTAL STRUCTURE, SULFUR-BRIDGING LIGAND, KEYWDS 2 NI-FE HYDROGENASE, REDUCED ENZYME, ATOMIC CAP AT ACTIVE KEYWDS 3 SITE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HIGUCHI,H.OGATA REVDAT 4 24-MAR-09 1H2R 1 ATOM CONECT REVDAT 3 24-FEB-09 1H2R 1 VERSN REVDAT 2 07-MAR-01 1H2R 1 HETATM REMARK REVDAT 1 05-JAN-00 1H2R 0 JRNL AUTH Y.HIGUCHI,H.OGATA,K.MIKI,N.YASUOKA,T.YAGI JRNL TITL REMOVAL OF THE BRIDGING LIGAND ATOM AT THE NI-FE JRNL TITL 2 ACTIVE SITE OF [NIFE] HYDROGENASE UPON REDUCTION JRNL TITL 3 WITH H2, AS REVEALED BY X-RAY STRUCTURE ANALYSIS JRNL TITL 4 AT 1.4 A RESOLUTION. JRNL EDIT W.A.HENDRICKSON, C.-I.BRANDEN JRNL REF STRUCTURE FOLD.DES. V. 7 549 1999 JRNL PUBL CURRENT BIOLOGY LTD JRNL REFN ISSN 0969-2126 JRNL PMID 10378274 JRNL DOI 10.1016/S0969-2126(99)80071-9 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.HIGUCHI,T.YAGI REMARK 1 TITL LIBERATION OF HYDROGEN SULFIDE DURING THE REMARK 1 TITL 2 CATALYTIC ACTION OF DESULFOVIBORIO HYDROGENASE REMARK 1 TITL 3 UNDER THE ATMOSPHERE OF HYDROGEN REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 255 295 1999 REMARK 1 PUBL ACADEMIC PRESS REMARK 1 REFN ISSN 0006-291X REMARK 1 DOI 10.1006/BBRC.1999.0210 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.HIGUCHI,T.YAGI,N.YASUOKA REMARK 1 TITL UNUSUAL LIGAND STRUCTURE IN NI-FE ACTIVE CENTER REMARK 1 TITL 2 AND AN ADDITIONAL MG SITE IN HYDROGENASE REVEALED REMARK 1 TITL 3 BY HIGH RESOLUTION X-RAY STRUCTURE ANALYSIS REMARK 1 EDIT W. A.HENDRICKSON, C-I BRANDEN REMARK 1 REF STRUCTURE V. 5 1671 1997 REMARK 1 PUBL CURRENT BIOLOGY LTD REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(97)00313-4 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 145719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10200 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13676 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 900 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 : 6194 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 577 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.96 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1H2R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB001181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 280 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.708 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 155198 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 91.6 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : 0.30000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: D-FOURIER REMARK 200 SOFTWARE USED: PROTEIN, MLPHARE (CCP4) REMARK 200 STARTING MODEL: 1H2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% MPD, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 50.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.34000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.43000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.34000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.43000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, L 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 O ILE S 147 O HOH S 3019 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OH TYR S 218 NH1 ARG L 487 2664 1.95 REMARK 500 O HOH L 3179 O HOH S 3054 2665 2.11 REMARK 500 O PRO S 263 O HOH L 3056 2664 2.13 REMARK 500 NE2 GLN S 266 O HOH L 3275 2664 2.14 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 LEU L 506 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 PRO S 4 -133.73 -77.34 REMARK 500 ARG S 5 -88.26 22.55 REMARK 500 ASN S 14 -123.11 -101.39 REMARK 500 THR S 18 0.21 82.03 REMARK 500 GLU S 29 79.66 40.97 REMARK 500 HIS S 45 98.63 -170.06 REMARK 500 LYS S 235 -179.95 62.20 REMARK 500 THR S 239 -20.30 -152.53 REMARK 500 CYS L 84 57.17 -93.24 REMARK 500 THR L 187 -82.63 -32.91 REMARK 500 ASN L 188 43.85 -99.01 REMARK 500 ALA L 231 -53.58 86.22 REMARK 500 HIS L 235 79.90 65.63 REMARK 500 GLN L 237 70.62 -150.65 REMARK 500 PHE L 238 -1.65 -141.32 REMARK 500 PHE L 302 69.90 76.35 REMARK 500 ARG L 322 15.08 56.20 REMARK 500 ALA L 347 11.27 -144.60 REMARK 500 LYS L 360 99.45 -163.14 REMARK 500 ASP L 363 166.36 76.29 REMARK 500 LEU L 364 107.95 -50.59 REMARK 500 TYR L 370 20.43 -145.44 REMARK 500 TYR L 378 -95.72 -80.31 REMARK 500 MET L 379 56.79 -95.19 REMARK 500 PRO L 533 60.13 -66.35 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 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: (11X,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 ARG S 5 22.6 L L OUTSIDE RANGE REMARK 500 VAL S 243 24.6 L L OUTSIDE RANGE REMARK 500 CYS S 252 24.4 L L OUTSIDE RANGE REMARK 500 THR L 56 24.8 L L OUTSIDE RANGE REMARK 500 THR L 85 23.2 L L OUTSIDE RANGE REMARK 500 THR L 187 24.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH L3047 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH S3109 DISTANCE = 8.42 ANGSTROMS REMARK 525 HOH L3079 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH L3108 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH S3236 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH S3241 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH S3306 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH L3178 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH S3440 DISTANCE = 5.74 ANGSTROMS REMARK 525 HOH S3455 DISTANCE = 10.49 ANGSTROMS REMARK 525 HOH S3509 DISTANCE = 5.62 ANGSTROMS REMARK 525 HOH S3520 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH S3524 DISTANCE = 7.95 ANGSTROMS REMARK 525 HOH L3266 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH L3298 DISTANCE = 8.19 ANGSTROMS REMARK 525 HOH L3352 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH L3387 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH L3401 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH L3478 DISTANCE = 5.45 ANGSTROMS REMARK 525 HOH L3503 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH L3539 DISTANCE = 6.04 ANGSTROMS 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 NFE L 1004 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 MG L1005 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 62 OE2 REMARK 620 2 LEU L 498 O 96.8 REMARK 620 3 HIS L 552 NE2 85.6 88.1 REMARK 620 4 HOH L3002 O 177.4 84.9 96.4 REMARK 620 5 HOH L3003 O 88.3 174.9 92.6 89.9 REMARK 620 6 HOH L3001 O 88.3 91.1 173.7 89.7 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NFE L1004 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 81 SG REMARK 620 2 CYS L 84 SG 96.3 REMARK 620 3 CYS L 546 SG 92.4 171.1 REMARK 620 4 CYS L 549 SG 108.3 79.3 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NFE L1004 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 84 SG REMARK 620 2 CYS L 549 SG 81.6 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 MG L 1005 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 S 1001 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 S 1002 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S S 1003 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NFE L 1004 DBREF 1H2R S 1 267 UNP P21853 PHNS_DESVM 51 317 DBREF 1H2R L 19 552 UNP P21852 PHNL_DESVM 19 552 SEQRES 1 S 267 LEU MET GLY PRO ARG ARG PRO SER VAL VAL TYR LEU HIS SEQRES 2 S 267 ASN ALA GLU CYS THR GLY CYS SER GLU SER VAL LEU ARG SEQRES 3 S 267 ALA PHE GLU PRO TYR ILE ASP THR LEU ILE LEU ASP THR SEQRES 4 S 267 LEU SER LEU ASP TYR HIS GLU THR ILE MET ALA ALA ALA SEQRES 5 S 267 GLY ASP ALA ALA GLU ALA ALA LEU GLU GLN ALA VAL ASN SEQRES 6 S 267 SER PRO HIS GLY PHE ILE ALA VAL VAL GLU GLY GLY ILE SEQRES 7 S 267 PRO THR ALA ALA ASN GLY ILE TYR GLY LYS VAL ALA ASN SEQRES 8 S 267 HIS THR MET LEU ASP ILE CYS SER ARG ILE LEU PRO LYS SEQRES 9 S 267 ALA GLN ALA VAL ILE ALA TYR GLY THR CYS ALA THR PHE SEQRES 10 S 267 GLY GLY VAL GLN ALA ALA LYS PRO ASN PRO THR GLY ALA SEQRES 11 S 267 LYS GLY VAL ASN ASP ALA LEU LYS HIS LEU GLY VAL LYS SEQRES 12 S 267 ALA ILE ASN ILE ALA GLY CYS PRO PRO ASN PRO TYR ASN SEQRES 13 S 267 LEU VAL GLY THR ILE VAL TYR TYR LEU LYS ASN LYS ALA SEQRES 14 S 267 ALA PRO GLU LEU ASP SER LEU ASN ARG PRO THR MET PHE SEQRES 15 S 267 PHE GLY GLN THR VAL HIS GLU GLN CYS PRO ARG LEU PRO SEQRES 16 S 267 HIS PHE ASP ALA GLY GLU PHE ALA PRO SER PHE GLU SER SEQRES 17 S 267 GLU GLU ALA ARG LYS GLY TRP CYS LEU TYR GLU LEU GLY SEQRES 18 S 267 CYS LYS GLY PRO VAL THR MET ASN ASN CYS PRO LYS ILE SEQRES 19 S 267 LYS PHE ASN GLN THR ASN TRP PRO VAL ASP ALA GLY HIS SEQRES 20 S 267 PRO CYS ILE GLY CYS SER GLU PRO ASP PHE TRP ASP ALA SEQRES 21 S 267 MET THR PRO PHE TYR GLN ASN SEQRES 1 L 534 SER SER TYR SER GLY PRO ILE VAL VAL ASP PRO VAL THR SEQRES 2 L 534 ARG ILE GLU GLY HIS LEU ARG ILE GLU VAL GLU VAL GLU SEQRES 3 L 534 ASN GLY LYS VAL LYS ASN ALA TYR SER SER SER THR LEU SEQRES 4 L 534 PHE ARG GLY LEU GLU ILE ILE LEU LYS GLY ARG ASP PRO SEQRES 5 L 534 ARG ASP ALA GLN HIS PHE THR GLN ARG THR CYS GLY VAL SEQRES 6 L 534 CYS THR TYR THR HIS ALA LEU ALA SER THR ARG CYS VAL SEQRES 7 L 534 ASP ASN ALA VAL GLY VAL HIS ILE PRO LYS ASN ALA THR SEQRES 8 L 534 TYR ILE ARG ASN LEU VAL LEU GLY ALA GLN TYR LEU HIS SEQRES 9 L 534 ASP HIS ILE VAL HIS PHE TYR HIS LEU HIS ALA LEU ASP SEQRES 10 L 534 PHE VAL ASP VAL THR ALA ALA LEU LYS ALA ASP PRO ALA SEQRES 11 L 534 LYS ALA ALA LYS VAL ALA SER SER ILE SER PRO ARG LYS SEQRES 12 L 534 THR THR ALA ALA ASP LEU LYS ALA VAL GLN ASP LYS LEU SEQRES 13 L 534 LYS THR PHE VAL GLU THR GLY GLN LEU GLY PRO PHE THR SEQRES 14 L 534 ASN ALA TYR PHE LEU GLY GLY HIS PRO ALA TYR TYR LEU SEQRES 15 L 534 ASP PRO GLU THR ASN LEU ILE ALA THR ALA HIS TYR LEU SEQRES 16 L 534 GLU ALA LEU ARG LEU GLN VAL LYS ALA ALA ARG ALA MET SEQRES 17 L 534 ALA VAL PHE GLY ALA LYS ASN PRO HIS THR GLN PHE THR SEQRES 18 L 534 VAL VAL GLY GLY VAL THR CYS TYR ASP ALA LEU THR PRO SEQRES 19 L 534 GLN ARG ILE ALA GLU PHE GLU ALA LEU TRP LYS GLU THR SEQRES 20 L 534 LYS ALA PHE VAL ASP GLU VAL TYR ILE PRO ASP LEU LEU SEQRES 21 L 534 VAL VAL ALA ALA ALA TYR LYS ASP TRP THR GLN TYR GLY SEQRES 22 L 534 GLY THR ASP ASN PHE ILE THR PHE GLY GLU PHE PRO LYS SEQRES 23 L 534 ASP GLU TYR ASP LEU ASN SER ARG PHE PHE LYS PRO GLY SEQRES 24 L 534 VAL VAL PHE LYS ARG ASP PHE LYS ASN ILE LYS PRO PHE SEQRES 25 L 534 ASP LYS MET GLN ILE GLU GLU HIS VAL ARG HIS SER TRP SEQRES 26 L 534 TYR GLU GLY ALA GLU ALA ARG HIS PRO TRP LYS GLY GLN SEQRES 27 L 534 THR GLN PRO LYS TYR THR ASP LEU HIS GLY ASP ASP ARG SEQRES 28 L 534 TYR SER TRP MET LYS ALA PRO ARG TYR MET GLY GLU PRO SEQRES 29 L 534 MET GLU THR GLY PRO LEU ALA GLN VAL LEU ILE ALA TYR SEQRES 30 L 534 SER GLN GLY HIS PRO LYS VAL LYS ALA VAL THR ASP ALA SEQRES 31 L 534 VAL LEU ALA LYS LEU GLY VAL GLY PRO GLU ALA LEU PHE SEQRES 32 L 534 SER THR LEU GLY ARG THR ALA ALA ARG GLY ILE GLU THR SEQRES 33 L 534 ALA VAL ILE ALA GLU TYR VAL GLY VAL MET LEU GLN GLU SEQRES 34 L 534 TYR LYS ASP ASN ILE ALA LYS GLY ASP ASN VAL ILE CYS SEQRES 35 L 534 ALA PRO TRP GLU MET PRO LYS GLN ALA GLU GLY VAL GLY SEQRES 36 L 534 PHE VAL ASN ALA PRO ARG GLY GLY LEU SER HIS TRP ILE SEQRES 37 L 534 ARG ILE GLU ASP GLY LYS ILE GLY ASN PHE GLN LEU VAL SEQRES 38 L 534 VAL PRO SER THR TRP THR LEU GLY PRO ARG CYS ASP LYS SEQRES 39 L 534 ASN ASN VAL SER PRO VAL GLU ALA SER LEU ILE GLY THR SEQRES 40 L 534 PRO VAL ALA ASP ALA LYS ARG PRO VAL GLU ILE LEU ARG SEQRES 41 L 534 THR VAL HIS SER PHE ASP PRO CYS ILE ALA CYS GLY VAL SEQRES 42 L 534 HIS HET MG L1005 1 HET SF4 S1001 8 HET SF4 S1002 8 HET F3S S1003 7 HET NFE L1004 8 HETNAM MG MAGNESIUM ION HETNAM SF4 IRON/SULFUR CLUSTER HETNAM F3S FE3-S4 CLUSTER HETNAM NFE NI-FE ACTIVE CENTER FORMUL 3 MG MG 2+ FORMUL 4 SF4 2(FE4 S4) FORMUL 6 F3S FE3 S4 FORMUL 7 NFE C2 H FE NI O3 S2 FORMUL 8 HOH *577(H2 O) HELIX 1 1 THR S 18 ARG S 26 1 9 HELIX 2 2 TYR S 31 ASP S 38 1 8 HELIX 3 3 ALA S 52 SER S 66 1 15 HELIX 4 4 ALA S 81 ILE S 85 5 5 HELIX 5 5 MET S 94 LEU S 102 1 9 HELIX 6 6 PRO S 103 ALA S 105 5 3 HELIX 7 7 GLY S 112 GLY S 118 1 7 HELIX 8 8 GLY S 119 ALA S 123 5 5 HELIX 9 9 GLY S 132 LEU S 137 1 6 HELIX 10 10 LYS S 138 GLY S 141 5 4 HELIX 11 11 ASN S 153 LYS S 168 1 16 HELIX 12 12 PRO S 179 GLY S 184 1 6 HELIX 13 13 VAL S 187 CYS S 191 5 5 HELIX 14 14 ARG S 193 ALA S 199 1 7 HELIX 15 15 SER S 208 LYS S 213 1 6 HELIX 16 16 LEU S 217 GLY S 221 5 5 HELIX 17 17 LYS S 223 THR S 227 5 5 HELIX 18 18 ASN S 230 LYS S 235 1 6 HELIX 19 19 TRP S 241 GLY S 246 5 6 HELIX 20 20 ASP S 256 MET S 261 1 6 HELIX 21 21 GLY L 60 LYS L 66 1 7 HELIX 22 22 ASP L 69 ARG L 71 5 3 HELIX 23 23 ASP L 72 ARG L 79 1 8 HELIX 24 24 TYR L 86 GLY L 101 1 16 HELIX 25 25 PRO L 105 LEU L 131 1 27 HELIX 26 26 HIS L 132 PHE L 136 5 5 HELIX 27 27 ASP L 138 ALA L 145 5 8 HELIX 28 28 ASP L 146 SER L 158 1 13 HELIX 29 29 THR L 163 THR L 180 1 18 HELIX 30 30 LEU L 183 THR L 187 5 5 HELIX 31 31 ASP L 201 ALA L 231 1 31 HELIX 32 32 CYS L 246 LEU L 250 5 5 HELIX 33 33 THR L 251 VAL L 272 1 22 HELIX 34 34 VAL L 272 TYR L 284 1 13 HELIX 35 35 LYS L 285 GLN L 289 5 5 HELIX 36 36 ASP L 308 ARG L 312 5 5 HELIX 37 37 ASP L 331 ILE L 335 5 5 HELIX 38 38 HIS L 351 GLY L 355 5 5 HELIX 39 39 GLY L 386 GLN L 397 1 12 HELIX 40 40 HIS L 399 GLY L 414 1 16 HELIX 41 41 GLY L 416 PHE L 421 5 6 HELIX 42 42 SER L 422 LYS L 454 1 33 HELIX 43 43 VAL L 500 GLY L 507 1 8 HELIX 44 44 SER L 516 LEU L 522 1 7 HELIX 45 45 PRO L 533 PHE L 543 1 11 HELIX 46 46 CYS L 546 HIS L 552 1 7 SHEET 1 A 5 SER S 41 TYR S 44 0 SHEET 2 A 5 SER S 8 HIS S 13 1 N VAL S 9 O SER S 41 SHEET 3 A 5 ILE S 71 GLU S 75 1 O ILE S 71 N VAL S 10 SHEET 4 A 5 ALA S 107 TYR S 111 1 O ALA S 107 N ALA S 72 SHEET 5 A 5 ILE S 145 ILE S 147 1 O ILE S 145 N ALA S 110 SHEET 1 B 2 ILE S 78 PRO S 79 0 SHEET 2 B 2 ALA S 130 LYS S 131 -1 O LYS S 131 N ILE S 78 SHEET 1 C 2 LYS S 88 VAL S 89 0 SHEET 2 C 2 HIS S 92 THR S 93 -1 N HIS S 92 O VAL S 89 SHEET 1 D 3 GLY L 23 VAL L 27 0 SHEET 2 D 3 LEU L 37 GLU L 44 -1 N ILE L 39 O VAL L 27 SHEET 3 D 3 LYS L 47 SER L 55 -1 O LYS L 47 N GLU L 44 SHEET 1 E 2 THR L 239 VAL L 240 0 SHEET 2 E 2 GLY L 243 VAL L 244 -1 N GLY L 243 O VAL L 240 SHEET 1 F 2 PHE L 296 THR L 298 0 SHEET 2 F 2 GLY L 317 VAL L 319 -1 N GLY L 317 O THR L 298 SHEET 1 G 2 GLU L 336 HIS L 338 0 SHEET 2 G 2 ALA L 375 ARG L 377 -1 O ALA L 375 N HIS L 338 SHEET 1 H 3 ALA L 469 ALA L 477 0 SHEET 2 H 3 GLY L 480 GLU L 489 -1 O GLY L 480 N ALA L 477 SHEET 3 H 3 LYS L 492 VAL L 499 -1 O LYS L 492 N GLU L 489 LINK ND1 HIS S 188 FE1 SF4 S1002 1555 1555 2.06 LINK SG CYS S 17 FE1 SF4 S1001 1555 1555 2.31 LINK SG CYS S 20 FE4 SF4 S1001 1555 1555 2.29 LINK SG CYS S 114 FE2 SF4 S1001 1555 1555 2.31 LINK SG CYS S 150 FE3 SF4 S1001 1555 1555 2.32 LINK SG CYS S 191 FE3 SF4 S1002 1555 1555 2.31 LINK SG CYS S 216 FE4 SF4 S1002 1555 1555 2.31 LINK SG CYS S 222 FE2 SF4 S1002 1555 1555 2.34 LINK SG CYS S 231 FE3 F3S S1003 1555 1555 2.35 LINK SG CYS S 249 FE1 F3S S1003 1555 1555 2.37 LINK OE2 GLU L 62 MG MG L1005 1555 1555 2.20 LINK SG CYS L 81 NI NFE L1004 1555 1555 2.32 LINK SG CYS L 84 NI NFE L1004 1555 1555 2.33 LINK SG CYS L 84 FE NFE L1004 1555 1555 2.29 LINK O LEU L 498 MG MG L1005 1555 1555 2.20 LINK SG CYS L 546 NI NFE L1004 1555 1555 2.24 LINK SG CYS L 549 NI NFE L1004 1555 1555 2.43 LINK SG CYS L 549 FE NFE L1004 1555 1555 2.36 LINK NE2 HIS L 552 MG MG L1005 1555 1555 2.19 LINK MG MG L1005 O HOH L3002 1555 1555 2.09 LINK MG MG L1005 O HOH L3003 1555 1555 2.11 LINK MG MG L1005 O HOH L3001 1555 1555 2.07 LINK SG CYS S 252 FE4 F3S S1003 1555 1555 2.31 CISPEP 1 GLU S 29 PRO S 30 0 0.40 CISPEP 2 LYS S 124 PRO S 125 0 0.13 CISPEP 3 CYS S 150 PRO S 151 0 -0.10 CISPEP 4 THR S 262 PRO S 263 0 0.16 CISPEP 5 ASP L 28 PRO L 29 0 0.36 CISPEP 6 ASN L 233 PRO L 234 0 0.35 SITE 1 AC1 6 GLU L 62 LEU L 498 HIS L 552 HOH L3001 SITE 2 AC1 6 HOH L3002 HOH L3003 SITE 1 AC2 10 ARG L 79 HIS L 235 GLU S 16 CYS S 17 SITE 2 AC2 10 CYS S 20 THR S 113 CYS S 114 GLY S 149 SITE 3 AC2 10 CYS S 150 PRO S 151 SITE 1 AC3 9 HIS S 188 CYS S 191 ARG S 193 LEU S 194 SITE 2 AC3 9 CYS S 216 LEU S 217 CYS S 222 HOH S3012 SITE 3 AC3 9 HOH S3338 SITE 1 AC4 11 LYS L 232 GLN L 237 ASN S 229 CYS S 231 SITE 2 AC4 11 PHE S 236 TRP S 241 CYS S 249 ILE S 250 SITE 3 AC4 11 CYS S 252 HOH S3184 HOH S3237 SITE 1 AC5 11 CYS L 81 CYS L 84 HIS L 88 ALA L 477 SITE 2 AC5 11 PRO L 478 ARG L 479 LEU L 482 PRO L 501 SITE 3 AC5 11 SER L 502 CYS L 546 CYS L 549 CRYST1 100.440 126.860 66.680 90.00 90.00 90.00 P 21 21 21 4 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 0.009956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007883 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014997 0.00000