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 MASTER 389 0 4 33 22 0 6 6 0 0 0 58 END