HEADER METAL BINDING PROTEIN/TRANSFERASE 02-OCT-12 3VYS TITLE CRYSTAL STRUCTURE OF THE HYPC-HYPD-HYPE COMPLEX (FORM I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPD; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK-HYPC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 10 ORGANISM_TAXID: 69014; SOURCE 11 STRAIN: KOD1; SOURCE 12 GENE: TK-HYPD; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 17 ORGANISM_TAXID: 69014; SOURCE 18 STRAIN: KOD1; SOURCE 19 GENE: TK1993; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS [NIFE] HYDROGENASE MATURATION, METAL BINDING PROTEIN-TRANSFERASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,K.MIKI REVDAT 3 08-NOV-23 3VYS 1 REMARK LINK REVDAT 2 31-JUL-13 3VYS 1 JRNL REVDAT 1 28-NOV-12 3VYS 0 JRNL AUTH S.WATANABE,R.MATSUMI,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL CRYSTAL STRUCTURES OF THE HYPCD COMPLEX AND THE HYPCDE JRNL TITL 2 TERNARY COMPLEX: TRANSIENT INTERMEDIATE COMPLEXES DURING JRNL TITL 3 [NIFE] HYDROGENASE MATURATION JRNL REF STRUCTURE V. 20 2124 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 23123111 JRNL DOI 10.1016/J.STR.2012.09.018 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2991081.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 32341 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1604 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5009 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 245 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5658 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.82000 REMARK 3 B22 (A**2) : 19.83000 REMARK 3 B33 (A**2) : -9.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.50 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 5.660 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.100 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.050 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 69.72 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : HYPD_FS10.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : HYPD_FS4.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 1.0000 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32417 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45400 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2Z1C, 2Z1D, 2Z1E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES, 12-16% PEG400, 10MM REMARK 280 MAGNESIUM CHLORIDE, PH 6.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.28350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.60050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.28350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.60050 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 52050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -215.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 0.00000 REMARK 350 BIOMT3 2 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 GLU A 55 REMARK 465 LYS A 56 REMARK 465 LYS A 57 REMARK 465 ALA A 58 REMARK 465 MET A 59 REMARK 465 GLU A 60 REMARK 465 ILE A 61 REMARK 465 LEU A 62 REMARK 465 GLU A 63 REMARK 465 ALA A 64 REMARK 465 TRP A 65 REMARK 465 ALA A 66 REMARK 465 GLU A 67 REMARK 465 VAL A 68 REMARK 465 GLU A 69 REMARK 465 LYS A 70 REMARK 465 ALA A 71 REMARK 465 MET A 72 REMARK 465 GLU A 73 REMARK 465 GLY A 74 REMARK 465 PHE A 75 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 PHE B 372 REMARK 465 MET C 1 REMARK 465 GLY C 2 REMARK 465 ARG C 336 REMARK 465 ILE C 337 REMARK 465 CYS C 338 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 LYS B 26 CG CD CE NZ REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 GLN B 165 CG CD OE1 NE2 REMARK 470 LYS B 210 CG CD CE NZ REMARK 470 GLU B 217 CG CD OE1 OE2 REMARK 470 GLU B 246 CG CD OE1 OE2 REMARK 470 GLU B 294 CG CD OE1 OE2 REMARK 470 LYS B 297 CG CD CE NZ REMARK 470 LYS B 300 CG CD CE NZ REMARK 470 LYS B 309 CG CD CE NZ REMARK 470 GLU B 311 CG CD OE1 OE2 REMARK 470 LYS B 314 CG CD CE NZ REMARK 470 LYS B 321 CG CD CE NZ REMARK 470 LYS B 343 CG CD CE NZ REMARK 470 GLU C 3 CG CD OE1 OE2 REMARK 470 GLU C 14 CG CD OE1 OE2 REMARK 470 GLU C 17 CG CD OE1 OE2 REMARK 470 ASP C 51 CG OD1 OD2 REMARK 470 LYS C 111 CG CD CE NZ REMARK 470 LYS C 115 CG CD CE NZ REMARK 470 LYS C 139 CG CD CE NZ REMARK 470 GLU C 153 CG CD OE1 OE2 REMARK 470 HIS C 154 CG ND1 CD2 CE1 NE2 REMARK 470 GLU C 185 CG CD OE1 OE2 REMARK 470 GLU C 214 CG CD OE1 OE2 REMARK 470 GLU C 295 CG CD OE1 OE2 REMARK 470 VAL C 334 CG1 CG2 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 A 15 21.38 -70.88 REMARK 500 PHE A 21 67.43 -104.78 REMARK 500 MET A 33 60.32 -153.05 REMARK 500 PRO B 64 48.44 -81.70 REMARK 500 VAL B 176 29.49 -140.86 REMARK 500 PHE B 194 130.68 -174.99 REMARK 500 TYR B 214 -14.14 -48.25 REMARK 500 TYR B 219 -2.99 -140.53 REMARK 500 LYS B 290 55.74 38.48 REMARK 500 LYS B 343 -91.15 -115.34 REMARK 500 VAL C 23 -70.36 -137.37 REMARK 500 GLU C 141 -86.14 70.52 REMARK 500 VAL C 197 122.47 -39.48 REMARK 500 ALA C 198 148.93 -178.67 REMARK 500 GLU C 209 4.35 -69.60 REMARK 500 LYS C 220 132.51 -179.20 REMARK 500 THR C 223 -110.97 -93.44 REMARK 500 ALA C 225 -2.17 82.18 REMARK 500 ALA C 301 142.16 -170.40 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 SF4 B 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 323 SG REMARK 620 2 SF4 B 501 S1 108.3 REMARK 620 3 SF4 B 501 S2 131.1 88.2 REMARK 620 4 SF4 B 501 S4 111.9 108.0 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 338 SG REMARK 620 2 SF4 B 501 S1 113.5 REMARK 620 3 SF4 B 501 S3 128.6 86.5 REMARK 620 4 SF4 B 501 S4 119.3 94.9 104.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 345 SG REMARK 620 2 SF4 B 501 S1 112.5 REMARK 620 3 SF4 B 501 S2 115.2 110.4 REMARK 620 4 SF4 B 501 S3 106.9 108.0 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 362 SG REMARK 620 2 SF4 B 501 S2 118.1 REMARK 620 3 SF4 B 501 S3 119.3 85.0 REMARK 620 4 SF4 B 501 S4 123.4 93.6 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 42 OD2 REMARK 620 2 ASP C 43 OD2 83.0 REMARK 620 3 ASP C 158 OD1 78.1 91.5 REMARK 620 4 MET C 219 O 158.9 87.9 83.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 43 OD1 REMARK 620 2 ASP C 84 OD1 97.0 REMARK 620 3 ASP C 221 OD1 75.3 89.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 59 OD2 REMARK 620 2 ASP C 84 OD2 75.9 REMARK 620 3 HOH C 701 O 91.2 161.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z1C RELATED DB: PDB REMARK 900 RELATED ID: 2Z1D RELATED DB: PDB REMARK 900 RELATED ID: 2Z1E RELATED DB: PDB REMARK 900 RELATED ID: 3VYR RELATED DB: PDB REMARK 900 RELATED ID: 3VYT RELATED DB: PDB REMARK 900 RELATED ID: 3VYU RELATED DB: PDB DBREF 3VYS A 2 75 UNP Q5JII0 Q5JII0_PYRKO 2 75 DBREF 3VYS B 1 372 UNP Q5JII1 Q5JII1_PYRKO 1 372 DBREF 3VYS C 1 338 UNP Q5JII7 Q5JII7_PYRKO 1 338 SEQRES 1 A 74 CYS LEU ALA VAL PRO GLY LYS VAL ILE GLU VAL ASN GLY SEQRES 2 A 74 PRO VAL ALA VAL VAL ASP PHE GLY GLY VAL LYS ARG GLU SEQRES 3 A 74 VAL ARG LEU ASP LEU MET PRO ASP THR LYS PRO GLY ASP SEQRES 4 A 74 TRP VAL ILE VAL HIS THR GLY PHE ALA ILE GLU LYS LEU SEQRES 5 A 74 ASP GLU LYS LYS ALA MET GLU ILE LEU GLU ALA TRP ALA SEQRES 6 A 74 GLU VAL GLU LYS ALA MET GLU GLY PHE SEQRES 1 B 372 MET GLU GLU PRO PHE GLU ALA TYR ARG SER ARG GLU VAL SEQRES 2 B 372 ALA MET LYS LEU VAL GLU LYS ILE ARG GLU GLU ALA LYS SEQRES 3 B 372 THR LEU ASP GLY GLU ILE ARG ILE MET HIS VAL CYS GLY SEQRES 4 B 372 THR HIS GLU ASP THR VAL THR ARG HIS GLY ILE ARG SER SEQRES 5 B 372 LEU LEU PRO GLU ASN VAL LYS VAL VAL SER GLY PRO GLY SEQRES 6 B 372 CYS PRO VAL CYS ILE THR PRO VAL GLU ASP ILE VAL ALA SEQRES 7 B 372 MET GLN LEU ILE MET ARG LYS ALA ARG GLU GLU GLY GLU SEQRES 8 B 372 GLU ILE ILE LEU THR THR PHE GLY ASP MET TYR LYS ILE SEQRES 9 B 372 PRO THR PRO MET GLY SER PHE ALA ASP LEU LYS SER GLU SEQRES 10 B 372 GLY PHE ASP VAL ARG ILE VAL TYR GLY ILE PHE ASP THR SEQRES 11 B 372 TYR ARG ILE ALA LYS GLU ASN PRO ASP LYS THR VAL VAL SEQRES 12 B 372 HIS PHE SER PRO GLY PHE GLU THR THR THR ALA PRO ALA SEQRES 13 B 372 ALA GLY MET LEU ASN VAL ALA ALA GLN GLU GLU LEU GLU SEQRES 14 B 372 ASN PHE LYS ILE TYR SER VAL HIS ARG LEU THR PRO PRO SEQRES 15 B 372 ALA VAL GLU VAL LEU LEU LYS GLN GLY THR VAL PHE GLN SEQRES 16 B 372 GLY LEU ILE ALA PRO GLY HIS VAL SER THR ILE ILE GLY SEQRES 17 B 372 VAL LYS GLY TRP GLU TYR LEU THR GLU LYS TYR GLY ILE SEQRES 18 B 372 PRO GLN VAL VAL ALA GLY PHE GLU PRO ASN ASP VAL LEU SEQRES 19 B 372 MET ALA ILE LEU MET LEU ILE ARG MET TYR LYS GLU GLY SEQRES 20 B 372 GLU ALA ARG ILE ILE ASN GLU TYR GLU ARG ALA VAL LYS SEQRES 21 B 372 TYR GLU GLY ASN VAL VAL ALA GLN LYS MET ILE ASP LYS SEQRES 22 B 372 PHE PHE GLU VAL VAL ASP ALA LYS TRP ARG ALA LEU GLY SEQRES 23 B 372 VAL PHE PRO LYS SER GLY LEU GLU LEU ARG LYS GLU TRP SEQRES 24 B 372 LYS ASP PHE GLU ILE ARG SER PHE TYR LYS VAL GLU VAL SEQRES 25 B 372 PRO LYS ASN LEU PRO ASP LEU GLU LYS GLY CYS ARG CYS SEQRES 26 B 372 GLY ALA VAL LEU ARG GLY LEU ALA LEU PRO THR ASP CYS SEQRES 27 B 372 PRO LEU PHE GLY LYS THR CYS THR PRO ARG HIS PRO VAL SEQRES 28 B 372 GLY PRO CYS MET VAL SER TYR GLU GLY THR CYS GLN ILE SEQRES 29 B 372 PHE TYR LYS TYR GLY VAL LEU PHE SEQRES 1 C 338 MET GLY GLU LYS ILE LYS LEU GLU HIS GLY ALA GLY GLY SEQRES 2 C 338 GLU ILE MET GLU GLU LEU LEU ARG ASP VAL ILE LEU LYS SEQRES 3 C 338 THR LEU THR LEU LYS SER ALA GLY GLY ILE GLY LEU ASP SEQRES 4 C 338 ALA LEU ASP ASP GLY ALA THR ILE PRO PHE GLY ASP LYS SEQRES 5 C 338 HIS ILE VAL PHE THR ILE ASP GLY HIS THR VAL LYS PRO SEQRES 6 C 338 LEU PHE PHE PRO GLY GLY ASP ILE GLY ARG LEU ALA VAL SEQRES 7 C 338 SER GLY THR VAL ASN ASP LEU ALA VAL MET GLY ALA GLU SEQRES 8 C 338 PRO ILE ALA LEU ALA ASN SER MET ILE ILE GLY GLU GLY SEQRES 9 C 338 LEU ASP MET GLU VAL LEU LYS ARG VAL LEU LYS SER MET SEQRES 10 C 338 ASP GLU THR ALA ARG GLU VAL PRO VAL PRO ILE VAL THR SEQRES 11 C 338 GLY ASP THR LYS VAL VAL GLU ASP LYS ILE GLU MET PHE SEQRES 12 C 338 VAL ILE THR ALA GLY ILE GLY ILE ALA GLU HIS PRO VAL SEQRES 13 C 338 SER ASP ALA GLY ALA LYS VAL GLY ASP ALA VAL LEU VAL SEQRES 14 C 338 SER GLY THR ILE GLY ASP HIS GLY ILE ALA LEU MET SER SEQRES 15 C 338 HIS ARG GLU GLY ILE ALA PHE GLU THR GLU LEU LYS SER SEQRES 16 C 338 ASP VAL ALA PRO ILE TRP ASP VAL VAL LYS ALA VAL ALA SEQRES 17 C 338 GLU THR ILE GLY TRP GLU ASN ILE HIS ALA MET LYS ASP SEQRES 18 C 338 PRO THR ARG ALA GLY LEU SER ASN ALA LEU ASN GLU ILE SEQRES 19 C 338 ALA ARG LYS SER ASN VAL GLY ILE LEU VAL ARG GLU ALA SEQRES 20 C 338 ASP ILE PRO ILE ARG PRO GLU VAL ARG ALA ALA SER GLU SEQRES 21 C 338 MET LEU GLY ILE SER PRO TYR ASP VAL ALA ASN GLU GLY SEQRES 22 C 338 LYS VAL VAL MET VAL VAL ALA ARG GLU TYR ALA GLU GLU SEQRES 23 C 338 ALA LEU GLU ALA MET ARG LYS THR GLU LYS GLY ARG ASN SEQRES 24 C 338 ALA ALA ILE ILE GLY GLU VAL ILE ALA ASP TYR ARG GLY SEQRES 25 C 338 LYS VAL LEU LEU GLU THR GLY ILE GLY GLY LYS ARG PHE SEQRES 26 C 338 MET GLU PRO PRO GLU GLY ASP PRO VAL PRO ARG ILE CYS HET SF4 B 501 8 HET MG C 601 1 HET MG C 602 1 HET MG C 603 1 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MG MAGNESIUM ION FORMUL 4 SF4 FE4 S4 FORMUL 5 MG 3(MG 2+) FORMUL 8 HOH *121(H2 O) HELIX 1 1 PHE B 5 ARG B 9 5 5 HELIX 2 2 SER B 10 THR B 27 1 18 HELIX 3 3 CYS B 38 HIS B 48 1 11 HELIX 4 4 GLY B 49 LEU B 54 5 6 HELIX 5 5 CYS B 66 THR B 71 1 6 HELIX 6 6 PRO B 72 GLU B 89 1 18 HELIX 7 7 PHE B 98 LYS B 103 1 6 HELIX 8 8 SER B 110 GLU B 117 1 8 HELIX 9 9 GLY B 126 ASN B 137 1 12 HELIX 10 10 PHE B 149 GLU B 167 1 19 HELIX 11 11 LEU B 179 LYS B 189 1 11 HELIX 12 12 PRO B 200 GLY B 208 1 9 HELIX 13 13 VAL B 209 GLY B 220 1 12 HELIX 14 14 GLU B 229 GLU B 246 1 18 HELIX 15 15 ASN B 264 PHE B 274 1 11 HELIX 16 16 LYS B 297 PHE B 307 5 11 HELIX 17 17 ARG B 324 ARG B 330 1 7 HELIX 18 18 LEU B 334 CYS B 338 5 5 HELIX 19 19 GLY B 352 SER B 357 1 6 HELIX 20 20 GLY B 360 GLY B 369 1 10 HELIX 21 21 LYS C 6 ALA C 11 5 6 HELIX 22 22 GLY C 13 VAL C 23 1 11 HELIX 23 23 VAL C 23 LEU C 28 1 6 HELIX 24 24 GLY C 37 LEU C 41 5 5 HELIX 25 25 ILE C 73 VAL C 87 1 15 HELIX 26 26 ASP C 106 VAL C 124 1 19 HELIX 27 27 GLY C 174 GLU C 185 1 12 HELIX 28 28 ILE C 200 GLY C 212 1 13 HELIX 29 29 ALA C 225 ASN C 239 1 15 HELIX 30 30 ALA C 247 ILE C 249 5 3 HELIX 31 31 ARG C 252 GLY C 263 1 12 HELIX 32 32 TYR C 283 LYS C 293 1 11 SHEET 1 A 7 ALA C 188 PHE C 189 0 SHEET 2 A 7 VAL A 24 ARG A 29 -1 N LYS A 25 O ALA C 188 SHEET 3 A 7 PHE A 48 LYS A 52 1 O ALA A 49 N ARG A 29 SHEET 4 A 7 TRP A 41 HIS A 45 -1 N HIS A 45 O PHE A 48 SHEET 5 A 7 VAL A 5 VAL A 12 -1 N GLY A 7 O VAL A 42 SHEET 6 A 7 VAL A 16 ASP A 20 -1 O VAL A 18 N ILE A 10 SHEET 7 A 7 VAL A 24 ARG A 29 -1 O VAL A 28 N ALA A 17 SHEET 1 B 3 VAL B 58 SER B 62 0 SHEET 2 B 3 ILE B 32 HIS B 36 1 N ILE B 34 O LYS B 59 SHEET 3 B 3 GLY B 196 ILE B 198 1 O GLY B 196 N MET B 35 SHEET 1 C 6 ASP B 120 ILE B 123 0 SHEET 2 C 6 ILE B 93 THR B 97 1 N LEU B 95 O ARG B 122 SHEET 3 C 6 THR B 141 GLY B 148 1 O THR B 141 N ILE B 94 SHEET 4 C 6 PHE B 171 ARG B 178 1 O VAL B 176 N SER B 146 SHEET 5 C 6 GLY B 286 LEU B 295 -1 O LEU B 293 N HIS B 177 SHEET 6 C 6 PHE B 275 TRP B 282 -1 N GLU B 276 O GLU B 294 SHEET 1 D 2 GLN B 223 VAL B 225 0 SHEET 2 D 2 ILE B 251 ASN B 253 1 O ILE B 252 N GLN B 223 SHEET 1 E 5 ALA C 45 PHE C 49 0 SHEET 2 E 5 LYS C 52 HIS C 61 -1 O PHE C 56 N ALA C 45 SHEET 3 E 5 MET C 142 ALA C 152 -1 O GLY C 150 N VAL C 55 SHEET 4 E 5 GLU C 91 GLY C 102 -1 N ALA C 96 O ALA C 147 SHEET 5 E 5 ILE C 128 VAL C 136 1 O LYS C 134 N ILE C 101 SHEET 1 F 2 PHE C 67 PHE C 68 0 SHEET 2 F 2 GLY C 71 ASP C 72 -1 O GLY C 71 N PHE C 68 SHEET 1 G 7 ILE C 216 LYS C 220 0 SHEET 2 G 7 VAL C 276 VAL C 279 -1 O VAL C 278 N ALA C 218 SHEET 3 G 7 ALA C 166 VAL C 169 -1 N LEU C 168 O MET C 277 SHEET 4 G 7 ALA C 301 ILE C 307 -1 O GLY C 304 N VAL C 167 SHEET 5 G 7 GLY C 241 ARG C 245 -1 N ARG C 245 O ILE C 303 SHEET 6 G 7 VAL C 314 GLU C 317 1 O GLU C 317 N VAL C 244 SHEET 7 G 7 LYS C 323 PHE C 325 -1 O ARG C 324 N LEU C 316 SSBOND 1 CYS B 66 CYS B 69 1555 1555 2.03 SSBOND 2 CYS B 325 CYS B 354 1555 1555 2.03 LINK SG CYS B 323 FE3 SF4 B 501 1555 1555 2.31 LINK SG CYS B 338 FE2 SF4 B 501 1555 1555 2.27 LINK SG CYS B 345 FE4 SF4 B 501 1555 1555 2.29 LINK SG CYS B 362 FE1 SF4 B 501 1555 1555 2.19 LINK OD2 ASP C 42 MG MG C 603 1555 1555 2.71 LINK OD1 ASP C 43 MG MG C 602 1555 1555 1.99 LINK OD2 ASP C 43 MG MG C 603 1555 1555 2.74 LINK OD2 ASP C 59 MG MG C 601 1555 1555 2.37 LINK OD2 ASP C 84 MG MG C 601 1555 1555 2.41 LINK OD1 ASP C 84 MG MG C 602 1555 1555 2.05 LINK OD1 ASP C 158 MG MG C 603 1555 1555 2.32 LINK O MET C 219 MG MG C 603 1555 1555 2.57 LINK OD1 ASP C 221 MG MG C 602 1555 1555 2.35 LINK MG MG C 601 O HOH C 701 1555 1555 2.93 CISPEP 1 LYS C 64 PRO C 65 0 -0.06 CISPEP 2 VAL C 124 PRO C 125 0 -1.76 SITE 1 AC1 8 CYS B 323 ARG B 324 CYS B 325 CYS B 338 SITE 2 AC1 8 CYS B 345 GLY B 352 MET B 355 CYS B 362 SITE 1 AC2 4 ASP C 59 ASP C 84 MG C 602 HOH C 701 SITE 1 AC3 4 ASP C 43 ASP C 84 ASP C 221 MG C 601 SITE 1 AC4 5 ASP C 42 ASP C 43 VAL C 87 ASP C 158 SITE 2 AC4 5 MET C 219 CRYST1 78.567 99.201 104.025 90.00 97.69 90.00 C 1 2 1 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 0.012728 0.000000 0.001717 0.00000 SCALE2 0.000000 0.010081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009700 0.00000