HEADER OXIDOREDUCTASE 10-MAY-17 5XLH TITLE CRYSTAL STRUCTURE OF AEROBICALLY PURIFIED AND AEROBICALLY CRYSTALLIZED TITLE 2 FOR 12WEEKS D. VULGARIS MIYAZAKI F [NIFE]-HYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT; COMPND 3 CHAIN: S; COMPND 4 FRAGMENT: UNP RESIDUES 51-317; COMPND 5 SYNONYM: NIFE HYDROGENLYASE SMALL CHAIN; COMPND 6 EC: 1.12.2.1; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT; COMPND 9 CHAIN: L; COMPND 10 FRAGMENT: UNP RESIDUES 1-552; COMPND 11 SYNONYM: NIFE HYDROGENLYASE LARGE CHAIN; COMPND 12 EC: 1.12.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI F / DSM SOURCE 3 19637); SOURCE 4 ORGANISM_TAXID: 883; SOURCE 5 STRAIN: MIYAZAKI F / DSM 19637; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI F / DSM SOURCE 8 19637); SOURCE 9 ORGANISM_TAXID: 883; SOURCE 10 STRAIN: MIYAZAKI F / DSM 19637 KEYWDS [NIFE]-HYDROGENASE D. VULGARIS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.NISHIKAWA,S.MOCHIDA,T.HIROMOTO,N.SHIBATA,Y.HIGUCHI REVDAT 1 06-JUN-18 5XLH 0 JRNL AUTH K.NISHIKAWA,S.MOCHIDA,T.HIROMOTO,N.SHIBATA,Y.HIGUCHI JRNL TITL NI-ELIMINATION FROM THE ACTIVE SITE OF THE STANDARD JRNL TITL 2 [NIFE]‐HYDROGENASE UPON OXIDATION BY O2. JRNL REF J. INORG. BIOCHEM. V. 177 435 2017 JRNL REFN ISSN 1873-3344 JRNL PMID 28967475 JRNL DOI 10.1016/J.JINORGBIO.2017.09.011 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 63427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3167 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.2970 - 5.4800 0.99 2810 146 0.1726 0.1909 REMARK 3 2 5.4800 - 4.3530 0.99 2693 139 0.1468 0.1742 REMARK 3 3 4.3530 - 3.8038 1.00 2676 141 0.1369 0.1603 REMARK 3 4 3.8038 - 3.4564 1.00 2658 140 0.1395 0.1844 REMARK 3 5 3.4564 - 3.2089 1.00 2621 138 0.1412 0.1661 REMARK 3 6 3.2089 - 3.0199 1.00 2639 139 0.1491 0.1883 REMARK 3 7 3.0199 - 2.8687 1.00 2632 139 0.1536 0.2021 REMARK 3 8 2.8687 - 2.7439 1.00 2628 138 0.1652 0.2345 REMARK 3 9 2.7439 - 2.6383 1.00 2599 137 0.1659 0.2283 REMARK 3 10 2.6383 - 2.5473 1.00 2610 137 0.1612 0.2114 REMARK 3 11 2.5473 - 2.4677 1.00 2603 137 0.1626 0.1965 REMARK 3 12 2.4677 - 2.3972 1.00 2599 137 0.1589 0.2248 REMARK 3 13 2.3972 - 2.3341 1.00 2624 138 0.1683 0.2433 REMARK 3 14 2.3341 - 2.2772 1.00 2589 136 0.1846 0.2237 REMARK 3 15 2.2772 - 2.2254 1.00 2585 137 0.1982 0.2684 REMARK 3 16 2.2254 - 2.1781 1.00 2601 137 0.1963 0.2394 REMARK 3 17 2.1781 - 2.1345 1.00 2598 136 0.2062 0.2669 REMARK 3 18 2.1345 - 2.0942 1.00 2569 135 0.2059 0.2551 REMARK 3 19 2.0942 - 2.0568 1.00 2613 137 0.2110 0.2794 REMARK 3 20 2.0568 - 2.0220 1.00 2550 135 0.2245 0.2712 REMARK 3 21 2.0220 - 1.9894 1.00 2613 137 0.2299 0.2781 REMARK 3 22 1.9894 - 1.9588 1.00 2575 136 0.2414 0.2830 REMARK 3 23 1.9588 - 1.9300 1.00 2575 135 0.2424 0.2751 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 6455 REMARK 3 ANGLE : 1.378 8812 REMARK 3 CHIRALITY : 0.079 955 REMARK 3 PLANARITY : 0.006 1147 REMARK 3 DIHEDRAL : 15.919 2328 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1300003727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS VII REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120962 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K 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 33.39500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.36000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.36000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.39500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.22000 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: 8700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 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 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 LEU S 1 REMARK 465 MET S 2 REMARK 465 GLY S 3 REMARK 465 MET L 1 REMARK 465 SER L 2 REMARK 465 GLY L 3 REMARK 465 CYS L 4 REMARK 465 ARG L 5 REMARK 465 ALA L 6 REMARK 465 GLN L 7 REMARK 465 ASN L 8 REMARK 465 ALA L 9 REMARK 465 PRO L 10 REMARK 465 GLY L 11 REMARK 465 GLY L 12 REMARK 465 ILE L 13 REMARK 465 PRO L 14 REMARK 465 VAL L 15 REMARK 465 THR L 16 REMARK 465 PRO L 17 REMARK 465 LYS L 18 REMARK 465 SER L 19 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 HOH S 1309 O HOH S 1320 2.16 REMARK 500 NZ LYS L 315 O HOH L 702 2.19 REMARK 500 O HOH L 1032 O HOH L 1109 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 L 549 CB CYS L 549 SG -0.103 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 ASN S 14 -123.29 -102.78 REMARK 500 GLU S 29 76.68 38.98 REMARK 500 HIS S 45 108.29 -161.19 REMARK 500 LYS S 235 179.99 56.83 REMARK 500 THR S 239 -29.09 -149.10 REMARK 500 CYS L 84 49.07 -81.41 REMARK 500 TYR L 86 -43.94 68.25 REMARK 500 ALA L 231 -47.40 81.57 REMARK 500 HIS L 235 84.70 67.07 REMARK 500 GLN L 237 67.39 -153.02 REMARK 500 PHE L 238 -8.66 -141.42 REMARK 500 VAL L 272 -60.53 -120.55 REMARK 500 PHE L 302 69.58 73.98 REMARK 500 ASP L 363 174.49 64.78 REMARK 500 TYR L 370 17.14 -145.38 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 S1360 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH S1361 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH L1186 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH L1187 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH L1188 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH L1189 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH L1190 DISTANCE = 6.76 ANGSTROMS 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 SF4 S1001 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 17 SG REMARK 620 2 SF4 S1001 S2 112.1 REMARK 620 3 SF4 S1001 S3 124.7 98.3 REMARK 620 4 SF4 S1001 S4 119.2 98.7 99.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1001 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 20 SG REMARK 620 2 SF4 S1001 S1 109.9 REMARK 620 3 SF4 S1001 S2 124.2 94.6 REMARK 620 4 SF4 S1001 S3 123.6 101.3 97.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1001 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 114 SG REMARK 620 2 SF4 S1001 S1 113.1 REMARK 620 3 SF4 S1001 S3 136.6 100.4 REMARK 620 4 SF4 S1001 S4 100.9 101.5 98.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1001 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 150 SG REMARK 620 2 SF4 S1001 S1 115.4 REMARK 620 3 SF4 S1001 S2 132.8 94.9 REMARK 620 4 SF4 S1001 S4 109.1 101.3 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1002 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS S 188 ND1 REMARK 620 2 SF4 S1002 S2 115.0 REMARK 620 3 SF4 S1002 S3 118.7 101.0 REMARK 620 4 SF4 S1002 S4 122.1 98.8 97.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1002 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 191 SG REMARK 620 2 SF4 S1002 S1 131.0 REMARK 620 3 SF4 S1002 S2 117.8 97.5 REMARK 620 4 SF4 S1002 S4 110.9 95.4 97.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1002 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 216 SG REMARK 620 2 SF4 S1002 S1 123.9 REMARK 620 3 SF4 S1002 S2 123.3 96.9 REMARK 620 4 SF4 S1002 S3 108.7 99.2 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 S1002 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 222 SG REMARK 620 2 SF4 S1002 S1 118.8 REMARK 620 3 SF4 S1002 S3 121.4 101.1 REMARK 620 4 SF4 S1002 S4 116.7 96.8 97.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S S1003 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 231 SG REMARK 620 2 F3S S1003 S1 117.7 REMARK 620 3 F3S S1003 S3 107.0 103.3 REMARK 620 4 F3S S1003 S4 109.5 115.3 102.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S S1003 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 249 SG REMARK 620 2 F3S S1003 S1 110.0 REMARK 620 3 F3S S1003 S2 111.0 111.1 REMARK 620 4 F3S S1003 S3 114.9 104.0 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S S1003 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS S 252 SG REMARK 620 2 F3S S1003 S2 114.1 REMARK 620 3 F3S S1003 S3 117.6 105.5 REMARK 620 4 F3S S1003 S4 103.3 112.9 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG L 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 62 OE2 REMARK 620 2 LEU L 498 O 98.1 REMARK 620 3 HOH L 772 O 86.1 91.3 REMARK 620 4 HOH L 811 O 176.1 80.9 90.2 REMARK 620 5 HOH L 740 O 90.6 170.9 86.6 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NFV L 601 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 81 SG REMARK 620 2 NFV L 601 O4 171.7 REMARK 620 3 CYS L 84 SG 103.8 82.1 REMARK 620 4 CSO L 546 SG 84.5 90.5 169.1 REMARK 620 5 CSO L 546 OD 73.8 106.0 137.4 37.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NFV L 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS L 84 SG REMARK 620 2 NFV L 601 C2 99.1 REMARK 620 3 NFV L 601 O4 82.7 92.9 REMARK 620 4 NFV L 601 C1 94.1 84.1 175.2 REMARK 620 5 NFV L 601 C3 166.7 92.2 89.7 94.1 REMARK 620 6 CYS L 549 SG 78.4 177.1 88.2 94.6 90.5 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 SF4 S 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 S 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F3S S 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD S 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NFV L 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG L 602 DBREF 5XLH S 1 267 UNP P21853 PHNS_DESVM 51 317 DBREF 5XLH L 1 552 UNP P21852 PHNL_DESVM 1 552 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 552 MET SER GLY CYS ARG ALA GLN ASN ALA PRO GLY GLY ILE SEQRES 2 L 552 PRO VAL THR PRO LYS SER SER TYR SER GLY PRO ILE VAL SEQRES 3 L 552 VAL ASP PRO VAL THR ARG ILE GLU GLY HIS LEU ARG ILE SEQRES 4 L 552 GLU VAL GLU VAL GLU ASN GLY LYS VAL LYS ASN ALA TYR SEQRES 5 L 552 SER SER SER THR LEU PHE ARG GLY LEU GLU ILE ILE LEU SEQRES 6 L 552 LYS GLY ARG ASP PRO ARG ASP ALA GLN HIS PHE THR GLN SEQRES 7 L 552 ARG THR CYS GLY VAL CYS THR TYR THR HIS ALA LEU ALA SEQRES 8 L 552 SER THR ARG CYS VAL ASP ASN ALA VAL GLY VAL HIS ILE SEQRES 9 L 552 PRO LYS ASN ALA THR TYR ILE ARG ASN LEU VAL LEU GLY SEQRES 10 L 552 ALA GLN TYR LEU HIS ASP HIS ILE VAL HIS PHE TYR HIS SEQRES 11 L 552 LEU HIS ALA LEU ASP PHE VAL ASP VAL THR ALA ALA LEU SEQRES 12 L 552 LYS ALA ASP PRO ALA LYS ALA ALA LYS VAL ALA SER SER SEQRES 13 L 552 ILE SER PRO ARG LYS THR THR ALA ALA ASP LEU LYS ALA SEQRES 14 L 552 VAL GLN ASP LYS LEU LYS THR PHE VAL GLU SER GLY GLN SEQRES 15 L 552 LEU GLY PRO PHE THR ASN ALA TYR PHE LEU GLY GLY HIS SEQRES 16 L 552 PRO ALA TYR TYR LEU ASP PRO GLU THR ASN LEU ILE ALA SEQRES 17 L 552 THR ALA HIS TYR LEU GLU ALA LEU ARG LEU GLN VAL LYS SEQRES 18 L 552 ALA ALA ARG ALA MET ALA VAL PHE GLY ALA LYS ASN PRO SEQRES 19 L 552 HIS THR GLN PHE THR VAL VAL GLY GLY VAL THR CYS TYR SEQRES 20 L 552 ASP ALA LEU THR PRO GLN ARG ILE ALA GLU PHE GLU ALA SEQRES 21 L 552 LEU TRP LYS GLU THR LYS ALA PHE VAL ASP GLU VAL TYR SEQRES 22 L 552 ILE PRO ASP LEU LEU VAL VAL ALA ALA ALA TYR LYS ASP SEQRES 23 L 552 TRP THR GLN TYR GLY GLY THR ASP ASN PHE ILE THR PHE SEQRES 24 L 552 GLY GLU PHE PRO LYS ASP GLU TYR ASP LEU ASN SER ARG SEQRES 25 L 552 PHE PHE LYS PRO GLY VAL VAL PHE LYS ARG ASP PHE LYS SEQRES 26 L 552 ASN ILE LYS PRO PHE ASP LYS MET GLN ILE GLU GLU HIS SEQRES 27 L 552 VAL ARG HIS SER TRP TYR GLU GLY ALA GLU ALA ARG HIS SEQRES 28 L 552 PRO TRP LYS GLY GLN THR GLN PRO LYS TYR THR ASP LEU SEQRES 29 L 552 HIS GLY ASP ASP ARG TYR SER TRP MET LYS ALA PRO ARG SEQRES 30 L 552 TYR MET GLY GLU PRO MET GLU THR GLY PRO LEU ALA GLN SEQRES 31 L 552 VAL LEU ILE ALA TYR SER GLN GLY HIS PRO LYS VAL LYS SEQRES 32 L 552 ALA VAL THR ASP ALA VAL LEU ALA LYS LEU GLY VAL GLY SEQRES 33 L 552 PRO GLU ALA LEU PHE SER THR LEU GLY ARG THR ALA ALA SEQRES 34 L 552 ARG GLY ILE GLU THR ALA VAL ILE ALA GLU TYR VAL GLY SEQRES 35 L 552 VAL MET LEU GLN GLU TYR LYS ASP ASN ILE ALA LYS GLY SEQRES 36 L 552 ASP ASN VAL ILE CYS ALA PRO TRP GLU MET PRO LYS GLN SEQRES 37 L 552 ALA GLU GLY VAL GLY PHE VAL ASN ALA PRO ARG GLY GLY SEQRES 38 L 552 LEU SER HIS TRP ILE ARG ILE GLU ASP GLY LYS ILE GLY SEQRES 39 L 552 ASN PHE GLN LEU VAL VAL PRO SER THR TRP THR LEU GLY SEQRES 40 L 552 PRO ARG CYS ASP LYS ASN LYS LEU SER PRO VAL GLU ALA SEQRES 41 L 552 SER LEU ILE GLY THR PRO VAL ALA ASP ALA LYS ARG PRO SEQRES 42 L 552 VAL GLU ILE LEU ARG THR VAL HIS SER PHE ASP PRO CSO SEQRES 43 L 552 ILE ALA CYS GLY VAL HIS MODRES 5XLH CSO L 546 CYS MODIFIED RESIDUE HET CSO L 546 7 HET SF4 S1001 8 HET SF4 S1002 8 HET F3S S1003 7 HET MPD S1004 8 HET NFV L 601 9 HET MG L 602 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM F3S FE3-S4 CLUSTER HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM NFV NI-FE OXIDIZED ACTIVE CENTER HETNAM MG MAGNESIUM ION FORMUL 2 CSO C3 H7 N O3 S FORMUL 3 SF4 2(FE4 S4) FORMUL 5 F3S FE3 S4 FORMUL 6 MPD C6 H14 O2 FORMUL 7 NFV C3 FE N2 NI O2 FORMUL 8 MG MG 2+ FORMUL 9 HOH *751(H2 O) HELIX 1 AA1 THR S 18 ARG S 26 1 9 HELIX 2 AA2 TYR S 31 ASP S 38 1 8 HELIX 3 AA3 ALA S 52 ASN S 65 1 14 HELIX 4 AA4 ALA S 81 ILE S 85 5 5 HELIX 5 AA5 MET S 94 LEU S 102 1 9 HELIX 6 AA6 PRO S 103 ALA S 105 5 3 HELIX 7 AA7 GLY S 112 GLY S 118 1 7 HELIX 8 AA8 GLY S 119 ALA S 123 5 5 HELIX 9 AA9 GLY S 132 LEU S 137 1 6 HELIX 10 AB1 LYS S 138 GLY S 141 5 4 HELIX 11 AB2 ASN S 153 LYS S 168 1 16 HELIX 12 AB3 PRO S 179 GLY S 184 1 6 HELIX 13 AB4 VAL S 187 CYS S 191 5 5 HELIX 14 AB5 ARG S 193 ALA S 199 1 7 HELIX 15 AB6 SER S 208 LYS S 213 1 6 HELIX 16 AB7 LYS S 223 THR S 227 5 5 HELIX 17 AB8 ASN S 230 LYS S 235 1 6 HELIX 18 AB9 ASP S 256 MET S 261 1 6 HELIX 19 AC1 GLY L 60 LYS L 66 1 7 HELIX 20 AC2 ASP L 69 ARG L 71 5 3 HELIX 21 AC3 ASP L 72 ARG L 79 1 8 HELIX 22 AC4 TYR L 86 GLY L 101 1 16 HELIX 23 AC5 PRO L 105 LEU L 131 1 27 HELIX 24 AC6 HIS L 132 PHE L 136 5 5 HELIX 25 AC7 VAL L 139 ALA L 145 5 7 HELIX 26 AC8 ASP L 146 SER L 158 1 13 HELIX 27 AC9 THR L 163 SER L 180 1 18 HELIX 28 AD1 LEU L 183 THR L 187 5 5 HELIX 29 AD2 ASP L 201 ALA L 231 1 31 HELIX 30 AD3 CYS L 246 LEU L 250 5 5 HELIX 31 AD4 THR L 251 VAL L 272 1 22 HELIX 32 AD5 VAL L 272 TYR L 284 1 13 HELIX 33 AD6 LYS L 285 GLN L 289 5 5 HELIX 34 AD7 ASP L 308 ARG L 312 5 5 HELIX 35 AD8 ASP L 323 ILE L 327 5 5 HELIX 36 AD9 ASP L 331 MET L 333 5 3 HELIX 37 AE1 HIS L 351 GLY L 355 5 5 HELIX 38 AE2 HIS L 365 ARG L 369 5 5 HELIX 39 AE3 GLY L 386 GLN L 397 1 12 HELIX 40 AE4 HIS L 399 GLY L 414 1 16 HELIX 41 AE5 GLY L 416 PHE L 421 5 6 HELIX 42 AE6 SER L 422 LYS L 454 1 33 HELIX 43 AE7 VAL L 500 GLY L 507 1 8 HELIX 44 AE8 SER L 516 ILE L 523 1 8 HELIX 45 AE9 PRO L 533 PHE L 543 1 11 HELIX 46 AF1 CSO L 546 HIS L 552 1 7 SHEET 1 AA1 5 SER S 41 TYR S 44 0 SHEET 2 AA1 5 SER S 8 HIS S 13 1 N VAL S 9 O SER S 41 SHEET 3 AA1 5 PHE S 70 GLU S 75 1 O ILE S 71 N SER S 8 SHEET 4 AA1 5 ALA S 107 TYR S 111 1 O ALA S 107 N ALA S 72 SHEET 5 AA1 5 ILE S 145 ILE S 147 1 O ILE S 145 N ALA S 110 SHEET 1 AA2 2 ILE S 78 PRO S 79 0 SHEET 2 AA2 2 ALA S 130 LYS S 131 -1 O LYS S 131 N ILE S 78 SHEET 1 AA3 2 LYS S 88 VAL S 89 0 SHEET 2 AA3 2 HIS S 92 THR S 93 -1 O HIS S 92 N VAL S 89 SHEET 1 AA4 3 GLY L 23 VAL L 27 0 SHEET 2 AA4 3 LEU L 37 GLU L 44 -1 O VAL L 43 N GLY L 23 SHEET 3 AA4 3 LYS L 47 SER L 55 -1 O SER L 54 N ARG L 38 SHEET 1 AA5 2 THR L 239 VAL L 240 0 SHEET 2 AA5 2 GLY L 243 VAL L 244 -1 O GLY L 243 N VAL L 240 SHEET 1 AA6 2 PHE L 296 THR L 298 0 SHEET 2 AA6 2 GLY L 317 VAL L 319 -1 O VAL L 319 N PHE L 296 SHEET 1 AA7 2 ILE L 335 HIS L 338 0 SHEET 2 AA7 2 ALA L 375 TYR L 378 -1 O ALA L 375 N HIS L 338 SHEET 1 AA8 3 GLN L 468 ALA L 477 0 SHEET 2 AA8 3 GLY L 480 GLU L 489 -1 O GLY L 480 N ALA L 477 SHEET 3 AA8 3 LYS L 492 VAL L 499 -1 O ASN L 495 N ARG L 487 SSBOND 1 CYS L 81 CYS L 84 1555 1555 2.03 LINK SG CYS S 17 FE1 SF4 S1001 1555 1555 2.29 LINK SG CYS S 20 FE4 SF4 S1001 1555 1555 2.35 LINK SG CYS S 114 FE2 SF4 S1001 1555 1555 2.36 LINK SG CYS S 150 FE3 SF4 S1001 1555 1555 2.34 LINK ND1 HIS S 188 FE1 SF4 S1002 1555 1555 2.26 LINK SG CYS S 191 FE3 SF4 S1002 1555 1555 2.38 LINK SG CYS S 216 FE4 SF4 S1002 1555 1555 2.44 LINK SG CYS S 222 FE2 SF4 S1002 1555 1555 2.31 LINK SG CYS S 231 FE3 F3S S1003 1555 1555 2.47 LINK SG CYS S 249 FE1 F3S S1003 1555 1555 2.46 LINK SG CYS S 252 FE4 F3S S1003 1555 1555 2.40 LINK OE2 GLU L 62 MG MG L 602 1555 1555 2.09 LINK SG ACYS L 81 NI ANFV L 601 1555 1555 2.41 LINK SG ACYS L 84 FE NFV L 601 1555 1555 2.46 LINK SG ACYS L 84 NI ANFV L 601 1555 1555 2.61 LINK O LEU L 498 MG MG L 602 1555 1555 2.13 LINK C PRO L 545 N CSO L 546 1555 1555 1.33 LINK SG CSO L 546 NI ANFV L 601 1555 1555 2.29 LINK C CSO L 546 N ILE L 547 1555 1555 1.33 LINK OD CSO L 546 NI ANFV L 601 1555 1555 2.72 LINK SG CYS L 549 FE NFV L 601 1555 1555 2.54 LINK MG MG L 602 O HOH L 772 1555 1555 2.02 LINK MG MG L 602 O HOH L 811 1555 1555 2.09 LINK MG MG L 602 O HOH L 740 1555 1555 2.06 CISPEP 1 GLU S 29 PRO S 30 0 5.11 CISPEP 2 LYS S 124 PRO S 125 0 4.85 CISPEP 3 CYS S 150 PRO S 151 0 2.49 CISPEP 4 THR S 262 PRO S 263 0 0.55 CISPEP 5 ASP L 28 PRO L 29 0 8.82 CISPEP 6 ASN L 233 PRO L 234 0 9.82 SITE 1 AC1 7 ARG L 79 CYS S 17 CYS S 20 THR S 113 SITE 2 AC1 7 CYS S 114 GLY S 149 CYS S 150 SITE 1 AC2 6 HIS S 188 CYS S 191 LEU S 194 CYS S 216 SITE 2 AC2 6 LEU S 217 CYS S 222 SITE 1 AC3 8 GLN L 237 ASN S 229 CYS S 231 PHE S 236 SITE 2 AC3 8 TRP S 241 CYS S 249 ILE S 250 CYS S 252 SITE 1 AC4 7 PHE L 320 LYS L 321 MET L 379 LEU S 194 SITE 2 AC4 7 PRO S 195 ASP S 198 HOH S1255 SITE 1 AC5 12 CYS L 81 CYS L 84 HIS L 88 ALA L 477 SITE 2 AC5 12 PRO L 478 ARG L 479 LEU L 482 VAL L 500 SITE 3 AC5 12 PRO L 501 SER L 502 CSO L 546 CYS L 549 SITE 1 AC6 6 GLU L 62 LEU L 498 HIS L 552 HOH L 740 SITE 2 AC6 6 HOH L 772 HOH L 811 CRYST1 66.790 98.440 126.720 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 0.014972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010158 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007891 0.00000