HEADER METAL BINDING PROTEIN 08-MAY-07 2Z1D TITLE CRYSTAL STRUCTURE OF [NIFE] HYDROGENASE MATURATION PROTEIN, HYPD FROM TITLE 2 THERMOCOCCUS KODAKARAENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: HYPD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS [NIFE] HYDROGENASE MATURATION, [4FE-4S] CLUSTER, THIOL REDOX, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,R.MATSUMI,T.ARAI,H.ATOMI,T.IMANAKA,K.MIKI REVDAT 4 12-NOV-14 2Z1D 1 HET HETATM HETNAM REVDAT 3 13-JUL-11 2Z1D 1 VERSN REVDAT 2 24-FEB-09 2Z1D 1 VERSN REVDAT 1 17-JUL-07 2Z1D 0 JRNL AUTH S.WATANABE,R.MATSUMI,T.ARAI,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL CRYSTAL STRUCTURES OF [NIFE] HYDROGENASE MATURATION PROTEINS JRNL TITL 2 HYPC, HYPD, AND HYPE: INSIGHTS INTO CYANATION REACTION BY JRNL TITL 3 THIOL REDOX SIGNALING JRNL REF MOL.CELL V. 27 29 2007 JRNL REFN ISSN 1097-2765 JRNL PMID 17612488 JRNL DOI 10.1016/J.MOLCEL.2007.05.039 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1556566.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 47451 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) : 0.179 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2794 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7294 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 458 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.92000 REMARK 3 B22 (A**2) : -4.39000 REMARK 3 B33 (A**2) : 7.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.000 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 58.03 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_REP.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : HYPD_FS4.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB027397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47481 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM TRIS-HCL, 160MM MGCL, 20% REMARK 280 PEG4000, 20% ETHYLENEGLYCOL, PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 59.19200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL UNIT IS MONOMER AND THE ASYMMETRIC UNIT REMARK 300 CONTAINS TWO BIOLOGICAL UNITS 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 PHE A 5 REMARK 465 GLU A 6 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLU B 3 REMARK 465 PRO B 4 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 TYR A 8 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 11 CG CD NE CZ NH1 NH2 REMARK 470 MET A 15 CG SD CE REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 TYR A 125 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 210 CG CD CE NZ REMARK 470 LYS A 269 CG CD CE NZ REMARK 470 LYS A 297 CG CD CE NZ REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 GLU A 311 CG CD OE1 OE2 REMARK 470 LYS A 343 CG CD CE NZ REMARK 470 ARG A 348 CG CD NE CZ NH1 NH2 REMARK 470 SER A 357 OG REMARK 470 PHE A 372 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE B 5 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 SER B 10 OG REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 ASP B 29 CG OD1 OD2 REMARK 470 GLU B 169 CG CD OE1 OE2 REMARK 470 VAL B 193 CG1 CG2 REMARK 470 LYS B 218 CG CD CE NZ REMARK 470 GLU B 246 CG CD OE1 OE2 REMARK 470 GLU B 248 CG CD OE1 OE2 REMARK 470 LYS B 269 CG CD CE NZ 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 ARG B 348 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 372 CG CD1 CD2 CE1 CE2 CZ 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 GLN A 190 31.70 -93.50 REMARK 500 THR A 192 100.93 -2.98 REMARK 500 ALA A 284 -1.64 71.31 REMARK 500 LYS A 343 -90.54 -104.22 REMARK 500 ASP B 29 -74.88 -63.41 REMARK 500 LYS B 290 45.08 36.89 REMARK 500 LYS B 343 -96.21 -100.88 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 A 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 323 SG REMARK 620 2 SF4 A 501 S1 106.7 REMARK 620 3 SF4 A 501 S2 125.9 102.9 REMARK 620 4 SF4 A 501 S4 114.5 100.5 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 338 SG REMARK 620 2 SF4 A 501 S1 112.9 REMARK 620 3 SF4 A 501 S3 119.6 101.3 REMARK 620 4 SF4 A 501 S4 108.7 107.5 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 345 SG REMARK 620 2 SF4 A 501 S1 118.1 REMARK 620 3 SF4 A 501 S2 115.3 107.2 REMARK 620 4 SF4 A 501 S3 111.9 99.5 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 362 SG REMARK 620 2 SF4 A 501 S2 116.4 REMARK 620 3 SF4 A 501 S3 112.4 105.0 REMARK 620 4 SF4 A 501 S4 115.5 105.1 100.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 323 SG REMARK 620 2 SF4 B 502 S2 123.3 REMARK 620 3 SF4 B 502 S3 114.7 104.3 REMARK 620 4 SF4 B 502 S4 105.8 105.0 101.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 338 SG REMARK 620 2 SF4 B 502 S1 122.7 REMARK 620 3 SF4 B 502 S3 107.2 101.2 REMARK 620 4 SF4 B 502 S4 111.2 106.2 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 345 SG REMARK 620 2 SF4 B 502 S1 114.6 REMARK 620 3 SF4 B 502 S2 117.2 104.0 REMARK 620 4 SF4 B 502 S4 115.8 101.2 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 502 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 362 SG REMARK 620 2 SF4 B 502 S1 111.8 REMARK 620 3 SF4 B 502 S2 118.4 107.5 REMARK 620 4 SF4 B 502 S3 115.3 99.6 102.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z1C RELATED DB: PDB REMARK 900 RELATED ID: 2Z1E RELATED DB: PDB REMARK 900 RELATED ID: 2Z1F RELATED DB: PDB DBREF 2Z1D A 1 372 UNP Q5JII1 Q5JII1_PYRKO 1 372 DBREF 2Z1D B 1 372 UNP Q5JII1 Q5JII1_PYRKO 1 372 SEQRES 1 A 372 MET GLU GLU PRO PHE GLU ALA TYR ARG SER ARG GLU VAL SEQRES 2 A 372 ALA MET LYS LEU VAL GLU LYS ILE ARG GLU GLU ALA LYS SEQRES 3 A 372 THR LEU ASP GLY GLU ILE ARG ILE MET HIS VAL CSD GLY SEQRES 4 A 372 THR HIS GLU ASP THR VAL THR ARG HIS GLY ILE ARG SER SEQRES 5 A 372 LEU LEU PRO GLU ASN VAL LYS VAL VAL SER GLY PRO GLY SEQRES 6 A 372 CYS PRO VAL CYS ILE THR PRO VAL GLU ASP ILE VAL ALA SEQRES 7 A 372 MET GLN LEU ILE MET ARG LYS ALA ARG GLU GLU GLY GLU SEQRES 8 A 372 GLU ILE ILE LEU THR THR PHE GLY ASP MET TYR LYS ILE SEQRES 9 A 372 PRO THR PRO MET GLY SER PHE ALA ASP LEU LYS SER GLU SEQRES 10 A 372 GLY PHE ASP VAL ARG ILE VAL TYR GLY ILE PHE ASP THR SEQRES 11 A 372 TYR ARG ILE ALA LYS GLU ASN PRO ASP LYS THR VAL VAL SEQRES 12 A 372 HIS PHE SER PRO GLY PHE GLU THR THR THR ALA PRO ALA SEQRES 13 A 372 ALA GLY MET LEU ASN VAL ALA ALA GLN GLU GLU LEU GLU SEQRES 14 A 372 ASN PHE LYS ILE TYR SER VAL HIS ARG LEU THR PRO PRO SEQRES 15 A 372 ALA VAL GLU VAL LEU LEU LYS GLN GLY THR VAL PHE GLN SEQRES 16 A 372 GLY LEU ILE ALA PRO GLY HIS VAL SER THR ILE ILE GLY SEQRES 17 A 372 VAL LYS GLY TRP GLU TYR LEU THR GLU LYS TYR GLY ILE SEQRES 18 A 372 PRO GLN VAL VAL ALA GLY PHE GLU PRO ASN ASP VAL LEU SEQRES 19 A 372 MET ALA ILE LEU MET LEU ILE ARG MET TYR LYS GLU GLY SEQRES 20 A 372 GLU ALA ARG ILE ILE ASN GLU TYR GLU ARG ALA VAL LYS SEQRES 21 A 372 TYR GLU GLY ASN VAL VAL ALA GLN LYS MET ILE ASP LYS SEQRES 22 A 372 PHE PHE GLU VAL VAL ASP ALA LYS TRP ARG ALA LEU GLY SEQRES 23 A 372 VAL PHE PRO LYS SER GLY LEU GLU LEU ARG LYS GLU TRP SEQRES 24 A 372 LYS ASP PHE GLU ILE ARG SER PHE TYR LYS VAL GLU VAL SEQRES 25 A 372 PRO LYS ASN LEU PRO ASP LEU GLU LYS GLY CYS ARG CYS SEQRES 26 A 372 GLY ALA VAL LEU ARG GLY LEU ALA LEU PRO THR ASP CYS SEQRES 27 A 372 PRO LEU PHE GLY LYS THR CYS THR PRO ARG HIS PRO VAL SEQRES 28 A 372 GLY PRO CYS MET VAL SER TYR GLU GLY THR CYS GLN ILE SEQRES 29 A 372 PHE TYR LYS TYR GLY VAL LEU 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 CSD 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 MODRES 2Z1D CSD A 38 CYS 3-SULFINOALANINE MODRES 2Z1D CSD B 38 CYS 3-SULFINOALANINE HET CSD A 38 16 HET CSD B 38 16 HET SF4 A 501 8 HET SF4 B 502 8 HETNAM CSD 3-SULFINOALANINE HETNAM SF4 IRON/SULFUR CLUSTER HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD 2(C3 H7 N O4 S) FORMUL 3 SF4 2(FE4 S4) FORMUL 5 HOH *580(H2 O) HELIX 1 1 ALA A 7 LYS A 26 1 20 HELIX 2 3 GLY A 49 LEU A 54 1 6 HELIX 3 4 PRO A 72 GLU A 89 1 18 HELIX 4 5 ASP A 100 ILE A 104 5 5 HELIX 5 6 SER A 110 GLU A 117 1 8 HELIX 6 7 GLY A 126 ASN A 137 1 12 HELIX 7 8 PHE A 149 GLU A 167 1 19 HELIX 8 9 LEU A 179 GLN A 190 1 12 HELIX 9 10 GLY A 201 GLY A 208 1 8 HELIX 10 11 VAL A 209 GLY A 220 1 12 HELIX 11 12 GLU A 229 GLU A 246 1 18 HELIX 12 13 ASN A 264 PHE A 274 1 11 HELIX 13 14 LYS A 297 PHE A 307 5 11 HELIX 14 15 ARG A 324 ARG A 330 1 7 HELIX 15 16 LEU A 334 CYS A 338 5 5 HELIX 16 17 GLY A 352 SER A 357 1 6 HELIX 17 18 GLY A 360 TYR A 368 1 9 HELIX 18 19 PHE B 5 LYS B 26 1 22 HELIX 19 21 GLY B 49 LEU B 54 1 6 HELIX 20 22 PRO B 72 GLU B 89 1 18 HELIX 21 23 ASP B 100 ILE B 104 5 5 HELIX 22 24 SER B 110 GLU B 117 1 8 HELIX 23 25 GLY B 126 ASN B 137 1 12 HELIX 24 26 PHE B 149 GLU B 167 1 19 HELIX 25 27 THR B 180 GLN B 190 1 11 HELIX 26 28 GLY B 201 LYS B 218 1 18 HELIX 27 29 GLU B 229 GLU B 246 1 18 HELIX 28 30 ASN B 264 PHE B 274 1 11 HELIX 29 31 LYS B 297 PHE B 307 5 11 HELIX 30 32 ARG B 324 ARG B 330 1 7 HELIX 31 33 LEU B 334 CYS B 338 5 5 HELIX 32 34 GLY B 352 SER B 357 1 6 HELIX 33 35 GLY B 360 TYR B 368 1 9 SHEET 1 A 5 VAL A 58 SER A 62 0 SHEET 2 A 5 ILE A 32 HIS A 36 1 N ILE A 34 O VAL A 61 SHEET 3 A 5 GLY A 196 PRO A 200 1 O ILE A 198 N MET A 35 SHEET 4 A 5 GLN A 223 ALA A 226 1 O VAL A 224 N LEU A 197 SHEET 5 A 5 ILE A 251 ASN A 253 1 O ILE A 252 N GLN A 223 SHEET 1 B 6 ASP A 120 ILE A 123 0 SHEET 2 B 6 ILE A 93 THR A 97 1 N LEU A 95 O ARG A 122 SHEET 3 B 6 THR A 141 GLY A 148 1 O VAL A 143 N THR A 96 SHEET 4 B 6 PHE A 171 ARG A 178 1 O LYS A 172 N VAL A 142 SHEET 5 B 6 GLY A 286 LEU A 295 -1 O LEU A 293 N HIS A 177 SHEET 6 B 6 PHE A 275 TRP A 282 -1 N VAL A 278 O GLY A 292 SHEET 1 C 5 VAL B 58 SER B 62 0 SHEET 2 C 5 ILE B 32 HIS B 36 1 N ILE B 34 O LYS B 59 SHEET 3 C 5 GLY B 196 PRO B 200 1 O ILE B 198 N MET B 35 SHEET 4 C 5 GLN B 223 ALA B 226 1 O VAL B 224 N LEU B 197 SHEET 5 C 5 ILE B 251 ASN B 253 1 O ILE B 252 N VAL B 225 SHEET 1 D 6 ASP B 120 ILE B 123 0 SHEET 2 D 6 ILE B 93 THR B 97 1 N LEU B 95 O ARG B 122 SHEET 3 D 6 THR B 141 GLY B 148 1 O VAL B 143 N THR B 96 SHEET 4 D 6 PHE B 171 ARG B 178 1 O LYS B 172 N VAL B 142 SHEET 5 D 6 GLY B 286 LEU B 295 -1 O LEU B 293 N HIS B 177 SHEET 6 D 6 PHE B 275 TRP B 282 -1 N GLU B 276 O GLU B 294 SSBOND 1 CYS A 66 CYS A 69 1555 1555 2.02 SSBOND 2 CYS A 325 CYS A 354 1555 1555 2.04 SSBOND 3 CYS B 66 CYS B 69 1555 1555 2.03 SSBOND 4 CYS B 325 CYS B 354 1555 1555 2.04 LINK SG CYS A 323 FE3 SF4 A 501 1555 1555 2.34 LINK SG CYS A 338 FE2 SF4 A 501 1555 1555 2.35 LINK SG CYS A 345 FE4 SF4 A 501 1555 1555 2.30 LINK SG CYS A 362 FE1 SF4 A 501 1555 1555 2.27 LINK SG CYS B 323 FE1 SF4 B 502 1555 1555 2.36 LINK SG CYS B 338 FE2 SF4 B 502 1555 1555 2.32 LINK SG CYS B 345 FE3 SF4 B 502 1555 1555 2.22 LINK SG CYS B 362 FE4 SF4 B 502 1555 1555 2.30 LINK C VAL A 37 N ACSD A 38 1555 1555 1.33 LINK C VAL A 37 N BCSD A 38 1555 1555 1.33 LINK C ACSD A 38 N GLY A 39 1555 1555 1.33 LINK C BCSD A 38 N GLY A 39 1555 1555 1.33 LINK C AVAL B 37 N ACSD B 38 1555 1555 1.33 LINK C BVAL B 37 N BCSD B 38 1555 1555 1.33 LINK C BCSD B 38 N GLY B 39 1555 1555 1.33 LINK C ACSD B 38 N GLY B 39 1555 1555 1.33 SITE 1 AC1 9 CYS A 323 ARG A 324 CYS A 325 CYS A 338 SITE 2 AC1 9 CYS A 345 GLY A 352 CYS A 354 MET A 355 SITE 3 AC1 9 CYS A 362 SITE 1 AC2 10 CYS B 323 ARG B 324 CYS B 325 CYS B 338 SITE 2 AC2 10 PHE B 341 CYS B 345 GLY B 352 CYS B 354 SITE 3 AC2 10 MET B 355 CYS B 362 CRYST1 42.253 118.384 81.165 90.00 100.89 90.00 P 1 21 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 0.023667 0.000000 0.004553 0.00000 SCALE2 0.000000 0.008447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012547 0.00000