HEADER METAL BINDING PROTEIN 02-OCT-12 3VYR TITLE CRYSTAL STRUCTURE OF THE HYPC-HYPD COMPLEX 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 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 KEYWDS [NIFE] HYDROGENASE MATURATION, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,K.MIKI REVDAT 3 08-NOV-23 3VYR 1 REMARK LINK REVDAT 2 31-JUL-13 3VYR 1 JRNL REVDAT 1 28-NOV-12 3VYR 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. 2.55 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1746755.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30494 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) : 0.170 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1545 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4773 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 240 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3430 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.74000 REMARK 3 B22 (A**2) : 8.74000 REMARK 3 B33 (A**2) : -17.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 7.070 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) : 6.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.550 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 9.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.520; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 63.79 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 : CIT_XPLOR_PAR4.PARAM REMARK 3 PARAMETER FILE 6 : 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 : CIT_XPLOR_TOP2.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VYR 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_1000095668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 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 : 30506 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48200 REMARK 200 FOR SHELL : 3.800 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: 2Z2C, 2Z1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M (NH4)3 CITRATE/CITRIC ACID(PH 4.5 REMARK 280 -4.7), 0.7% 2-METHYL-2,4-PENTANDIOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K, PH 4.7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 CYS A 2 REMARK 465 LEU A 3 REMARK 465 MET B 1 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 56 CG CD CE NZ REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 ARG B 11 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 GLU B 88 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 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 B 64 40.84 -82.35 REMARK 500 PRO B 107 -6.26 -57.10 REMARK 500 ALA B 284 -4.90 70.84 REMARK 500 LYS B 290 52.25 39.80 REMARK 500 LYS B 343 -92.58 -115.51 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 111.5 REMARK 620 3 SF4 B 501 S2 125.7 88.7 REMARK 620 4 SF4 B 501 S4 115.0 106.2 105.6 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 117.2 REMARK 620 3 SF4 B 501 S3 128.2 85.3 REMARK 620 4 SF4 B 501 S4 115.7 95.4 106.7 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 114.8 REMARK 620 3 SF4 B 501 S2 109.7 111.6 REMARK 620 4 SF4 B 501 S3 105.6 106.7 108.0 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 113.2 REMARK 620 3 SF4 B 501 S3 118.5 85.6 REMARK 620 4 SF4 B 501 S4 126.6 94.7 107.8 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 CIT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 507 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: 3VYS RELATED DB: PDB REMARK 900 RELATED ID: 3VYT RELATED DB: PDB REMARK 900 RELATED ID: 3VYU RELATED DB: PDB DBREF 3VYR A 2 75 UNP Q5JII0 Q5JII0_PYRKO 2 75 DBREF 3VYR B 1 372 UNP Q5JII1 Q5JII1_PYRKO 1 372 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 HET CIT A 101 13 HET SF4 B 501 8 HET CIT B 502 13 HET CIT B 503 13 HET CIT B 504 13 HET CIT B 505 13 HET CIT B 506 13 HET CIT B 507 13 HETNAM CIT CITRIC ACID HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 3 CIT 7(C6 H8 O7) FORMUL 4 SF4 FE4 S4 FORMUL 11 HOH *138(H2 O) HELIX 1 1 ASP A 54 GLY A 74 1 21 HELIX 2 2 PHE B 5 ARG B 9 5 5 HELIX 3 3 SER B 10 THR B 27 1 18 HELIX 4 4 CYS B 38 HIS B 48 1 11 HELIX 5 5 GLY B 49 LEU B 54 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 THR B 180 GLN B 190 1 11 HELIX 12 12 GLY B 201 GLY B 208 1 8 HELIX 13 13 VAL B 209 GLY B 211 5 3 HELIX 14 14 TRP B 212 GLY B 220 1 9 HELIX 15 15 GLU B 229 GLU B 246 1 18 HELIX 16 16 ASN B 264 PHE B 274 1 11 HELIX 17 17 LYS B 297 TYR B 308 5 12 HELIX 18 18 ARG B 324 ARG B 330 1 7 HELIX 19 19 LEU B 334 CYS B 338 5 5 HELIX 20 20 GLY B 352 SER B 357 1 6 HELIX 21 21 GLY B 360 TYR B 368 1 9 SHEET 1 A 6 GLY A 7 ASN A 13 0 SHEET 2 A 6 VAL A 16 PHE A 21 -1 O ASP A 20 N LYS A 8 SHEET 3 A 6 VAL A 24 ARG A 29 -1 O VAL A 24 N PHE A 21 SHEET 4 A 6 PHE A 48 LYS A 52 1 O ALA A 49 N ARG A 29 SHEET 5 A 6 TRP A 41 HIS A 45 -1 N HIS A 45 O PHE A 48 SHEET 6 A 6 GLY A 7 ASN A 13 -1 N GLY A 7 O VAL A 42 SHEET 1 B 5 VAL B 58 SER B 62 0 SHEET 2 B 5 ILE B 32 HIS B 36 1 N ILE B 34 O LYS B 59 SHEET 3 B 5 GLY B 196 PRO B 200 1 O ILE B 198 N MET B 35 SHEET 4 B 5 GLN B 223 ALA B 226 1 O VAL B 224 N LEU B 197 SHEET 5 B 5 ILE B 251 ASN B 253 1 O ILE B 252 N GLN B 223 SHEET 1 C 6 VAL B 121 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 VAL B 143 N THR B 96 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 ALA B 280 O PHE B 288 SSBOND 1 CYS B 66 CYS B 69 1555 1555 2.02 SSBOND 2 CYS B 325 CYS B 354 1555 1555 2.04 LINK SG CYS B 323 FE3 SF4 B 501 1555 1555 2.28 LINK SG CYS B 338 FE2 SF4 B 501 1555 1555 2.25 LINK SG CYS B 345 FE4 SF4 B 501 1555 1555 2.31 LINK SG CYS B 362 FE1 SF4 B 501 1555 1555 2.26 SITE 1 AC1 6 LYS A 25 ARG A 26 GLU A 27 HOH A 216 SITE 2 AC1 6 LEU B 188 TYR B 219 SITE 1 AC2 8 CYS B 323 ARG B 324 CYS B 325 CYS B 338 SITE 2 AC2 8 CYS B 345 GLY B 352 MET B 355 CYS B 362 SITE 1 AC3 8 HIS A 45 VAL B 68 PHE B 98 ASP B 100 SITE 2 AC3 8 THR B 152 TYR B 358 GLU B 359 CIT B 504 SITE 1 AC4 4 ASP B 75 ALA B 78 TYR B 174 ARG B 305 SITE 1 AC5 14 HIS A 45 CYS B 38 THR B 40 GLY B 65 SITE 2 AC5 14 PRO B 67 PHE B 149 THR B 151 THR B 152 SITE 3 AC5 14 HIS B 202 VAL B 203 GLU B 359 CIT B 502 SITE 4 AC5 14 HOH B 626 HOH B 676 SITE 1 AC6 6 ASP A 20 GLY A 23 LEU B 28 ASP B 29 SITE 2 AC6 6 TYR B 244 LYS B 245 SITE 1 AC7 9 ALA A 4 PRO A 6 LEU A 53 PRO B 4 SITE 2 AC7 9 PHE B 5 ARG B 9 GLU B 229 TYR B 255 SITE 3 AC7 9 ARG B 257 SITE 1 AC8 4 GLU A 60 SER B 10 ARG B 11 GLU B 12 CRYST1 181.179 181.179 49.433 90.00 90.00 120.00 P 3 2 1 6 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 0.005519 0.003187 0.000000 0.00000 SCALE2 0.000000 0.006373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020229 0.00000