HEADER RNA 05-DEC-16 5MKO TITLE [2FE-2S] CLUSTER CONTAINING TTUA IN COMPLEX WITH AMP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TTUA PH0300; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII (STRAIN ATCC 700860 / DSM SOURCE 3 12428 / JCM 9974 / NBRC 100139 / OT-3); SOURCE 4 ORGANISM_TAXID: 70601; SOURCE 5 GENE: PH0300; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBG102 KEYWDS TTUA, PH0300, AMP, 2FE-2S, THIOLATION, TRNA MODIFICATION ENZYME, [FE- KEYWDS 2 S] CLUSTER, IRON-SULFUR CLUSTER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.ARRAGAIN,O.BIMAI,P.LEGRAND,B.GOLINELLI-PIMPANEAU REVDAT 6 17-JAN-24 5MKO 1 REMARK REVDAT 5 06-SEP-17 5MKO 1 REMARK REVDAT 4 19-JUL-17 5MKO 1 REVDAT 3 12-JUL-17 5MKO 1 REVDAT 2 28-JUN-17 5MKO 1 JRNL REVDAT 1 14-JUN-17 5MKO 0 JRNL AUTH S.ARRAGAIN,O.BIMAI,P.LEGRAND,S.CAILLAT,J.L.RAVANAT,N.TOUATI, JRNL AUTH 2 L.BINET,M.ATTA,M.FONTECAVE,B.GOLINELLI-PIMPANEAU JRNL TITL NONREDOX THIOLATION IN TRNA OCCURRING VIA SULFUR ACTIVATION JRNL TITL 2 BY A [4FE-4S] CLUSTER. JRNL REF PROC. NATL. ACAD. SCI. V. 114 7355 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28655838 JRNL DOI 10.1073/PNAS.1700902114 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 17292 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 + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 878 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.18 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1499 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2510 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1413 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.74 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4927 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24550 REMARK 3 B22 (A**2) : 7.20490 REMARK 3 B33 (A**2) : -7.45040 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) : 0.400 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.349 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5089 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6831 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1852 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 107 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 744 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5089 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 3 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 644 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5671 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.33 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.55 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { *|* } REMARK 3 ORIGIN FOR THE GROUP (A): -4.3493 22.6674 15.9846 REMARK 3 T TENSOR REMARK 3 T11: -0.0691 T22: 0.0862 REMARK 3 T33: -0.0925 T12: 0.0433 REMARK 3 T13: -0.0377 T23: -0.0339 REMARK 3 L TENSOR REMARK 3 L11: 0.7245 L22: 0.9436 REMARK 3 L33: 1.8825 L12: 0.2437 REMARK 3 L13: -0.2330 L23: -0.3236 REMARK 3 S TENSOR REMARK 3 S11: -0.0400 S12: 0.0589 S13: 0.0896 REMARK 3 S21: 0.0177 S22: -0.0027 S23: 0.1024 REMARK 3 S31: -0.1957 S32: -0.0897 S33: 0.0427 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200001704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17292 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 4.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3VRH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 3350, 2.5% DMF, NACL 0.2M, PH REMARK 280 9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 34.43000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.14000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.14000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.43000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.16000 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: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 PHE A 308 REMARK 465 GLY A 309 REMARK 465 PRO A 310 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 ALA B 223 REMARK 465 ARG B 224 REMARK 465 ASP B 304 REMARK 465 GLU B 305 REMARK 465 GLU B 306 REMARK 465 PRO B 307 REMARK 465 PHE B 308 REMARK 465 GLY B 309 REMARK 465 PRO B 310 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 SER A 7 47.75 -89.96 REMARK 500 TYR A 86 -46.00 -132.28 REMARK 500 ALA A 226 61.02 -116.23 REMARK 500 PRO A 262 5.54 -66.71 REMARK 500 LYS A 265 9.06 51.30 REMARK 500 SER A 301 -65.46 -120.17 REMARK 500 SER B 7 47.32 -89.62 REMARK 500 TYR B 86 -54.04 -135.76 REMARK 500 LYS B 122 88.60 -68.77 REMARK 500 GLU B 218 111.61 -34.46 REMARK 500 ALA B 226 59.22 -115.83 REMARK 500 PRO B 262 0.72 -65.84 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 CYS A 6 SG 122.0 REMARK 620 3 CYS A 22 SG 129.0 94.1 REMARK 620 4 HIS A 25 ND1 109.2 99.3 97.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 404 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 128 SG REMARK 620 2 FES A 404 S1 103.6 REMARK 620 3 FES A 404 S2 123.1 104.1 REMARK 620 4 CYS A 220 SG 137.1 80.8 95.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 404 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 131 SG REMARK 620 2 FES A 404 S1 115.1 REMARK 620 3 FES A 404 S2 114.0 104.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 272 SG REMARK 620 2 CYS A 275 SG 104.0 REMARK 620 3 CYS A 284 SG 111.4 112.6 REMARK 620 4 CYS A 287 SG 113.2 100.0 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 3 SG REMARK 620 2 CYS B 6 SG 124.2 REMARK 620 3 CYS B 22 SG 127.3 96.8 REMARK 620 4 HIS B 25 ND1 105.8 100.5 96.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 404 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 128 SG REMARK 620 2 FES B 404 S1 101.9 REMARK 620 3 FES B 404 S2 121.9 104.4 REMARK 620 4 CYS B 220 SG 113.2 93.0 116.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES B 404 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 131 SG REMARK 620 2 FES B 404 S1 115.3 REMARK 620 3 FES B 404 S2 117.2 104.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 272 SG REMARK 620 2 CYS B 275 SG 102.0 REMARK 620 3 CYS B 284 SG 112.4 115.0 REMARK 620 4 CYS B 287 SG 110.5 98.7 116.6 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 AMP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FES A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FES B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VRH RELATED DB: PDB REMARK 900 3VRH CONTAINS THE SAME PROTEIN WITHOUT AMP AND WITHOUT THE [2FE-2S] REMARK 900 CLUSTER. DBREF 5MKO A 1 310 UNP O58038 O58038_PYRHO 1 310 DBREF 5MKO B 1 310 UNP O58038 O58038_PYRHO 1 310 SEQADV 5MKO GLY A -2 UNP O58038 EXPRESSION TAG SEQADV 5MKO SER A -1 UNP O58038 EXPRESSION TAG SEQADV 5MKO SER A 0 UNP O58038 EXPRESSION TAG SEQADV 5MKO GLY B -2 UNP O58038 EXPRESSION TAG SEQADV 5MKO SER B -1 UNP O58038 EXPRESSION TAG SEQADV 5MKO SER B 0 UNP O58038 EXPRESSION TAG SEQRES 1 A 313 GLY SER SER MET LYS CYS LYS PHE CYS SER ARG GLU ALA SEQRES 2 A 313 TYR ILE LYS ILE HIS TYR PRO LYS MET TYR LEU CYS GLU SEQRES 3 A 313 GLU HIS PHE LYS GLU TYR PHE GLU ARG LYS VAL SER ARG SEQRES 4 A 313 THR ILE GLU ARG TYR LYS LEU LEU THR LYS ASP GLU ARG SEQRES 5 A 313 ILE LEU VAL ALA VAL SER GLY GLY LYS ASP SER ALA VAL SEQRES 6 A 313 THR ALA TYR VAL LEU LYS LYS LEU GLY TYR ASN ILE GLU SEQRES 7 A 313 CYS LEU HIS ILE ASN LEU GLY ILE SER GLY TYR SER GLU SEQRES 8 A 313 LYS SER GLU GLU TYR ALA LYS LYS GLN CYS LYS LEU ILE SEQRES 9 A 313 GLY ALA PRO LEU HIS ILE VAL ARG ILE LYS GLU ILE LEU SEQRES 10 A 313 GLY TYR GLY ILE GLY GLU VAL LYS THR ARG ARG PRO PRO SEQRES 11 A 313 CYS SER TYR CYS GLY LEU THR LYS ARG TYR ILE MET ASN SEQRES 12 A 313 LYS PHE ALA TYR ASP ASN GLY PHE ASP ALA ILE ALA THR SEQRES 13 A 313 GLY HIS ASN LEU ASP ASP GLU ALA SER PHE LEU LEU ASN SEQRES 14 A 313 ASN ILE LEU HIS TRP ASN THR GLU TYR LEU ALA LYS GLY SEQRES 15 A 313 GLY PRO ILE LEU PRO GLN GLN GLY LYS PHE ILE LYS LYS SEQRES 16 A 313 VAL LYS PRO LEU TYR GLU VAL THR GLU ARG GLU VAL VAL SEQRES 17 A 313 ALA TYR ALA LEU ALA VAL GLY LEU GLU TYR ILE VAL GLU SEQRES 18 A 313 GLU CYS PRO TYR ALA ARG GLY ALA THR THR LEU ASP MET SEQRES 19 A 313 LYS GLY VAL LEU ASN GLU LEU GLU GLU LYS ARG PRO GLY SEQRES 20 A 313 THR LYS PHE ASN PHE VAL ARG GLY TYR LEU LYS LYS LYS SEQRES 21 A 313 LYS LEU PHE GLU PRO GLU ILE LYS GLU LYS GLU ILE LYS SEQRES 22 A 313 GLU CYS LYS ILE CYS ARG MET PRO SER SER GLY ASP ILE SEQRES 23 A 313 CYS ALA PHE CYS LYS PHE TRP GLY LEU LYS LYS GLU ILE SEQRES 24 A 313 ASN PHE LYS VAL SER SER THR ASP GLU GLU PRO PHE GLY SEQRES 25 A 313 PRO SEQRES 1 B 313 GLY SER SER MET LYS CYS LYS PHE CYS SER ARG GLU ALA SEQRES 2 B 313 TYR ILE LYS ILE HIS TYR PRO LYS MET TYR LEU CYS GLU SEQRES 3 B 313 GLU HIS PHE LYS GLU TYR PHE GLU ARG LYS VAL SER ARG SEQRES 4 B 313 THR ILE GLU ARG TYR LYS LEU LEU THR LYS ASP GLU ARG SEQRES 5 B 313 ILE LEU VAL ALA VAL SER GLY GLY LYS ASP SER ALA VAL SEQRES 6 B 313 THR ALA TYR VAL LEU LYS LYS LEU GLY TYR ASN ILE GLU SEQRES 7 B 313 CYS LEU HIS ILE ASN LEU GLY ILE SER GLY TYR SER GLU SEQRES 8 B 313 LYS SER GLU GLU TYR ALA LYS LYS GLN CYS LYS LEU ILE SEQRES 9 B 313 GLY ALA PRO LEU HIS ILE VAL ARG ILE LYS GLU ILE LEU SEQRES 10 B 313 GLY TYR GLY ILE GLY GLU VAL LYS THR ARG ARG PRO PRO SEQRES 11 B 313 CYS SER TYR CYS GLY LEU THR LYS ARG TYR ILE MET ASN SEQRES 12 B 313 LYS PHE ALA TYR ASP ASN GLY PHE ASP ALA ILE ALA THR SEQRES 13 B 313 GLY HIS ASN LEU ASP ASP GLU ALA SER PHE LEU LEU ASN SEQRES 14 B 313 ASN ILE LEU HIS TRP ASN THR GLU TYR LEU ALA LYS GLY SEQRES 15 B 313 GLY PRO ILE LEU PRO GLN GLN GLY LYS PHE ILE LYS LYS SEQRES 16 B 313 VAL LYS PRO LEU TYR GLU VAL THR GLU ARG GLU VAL VAL SEQRES 17 B 313 ALA TYR ALA LEU ALA VAL GLY LEU GLU TYR ILE VAL GLU SEQRES 18 B 313 GLU CYS PRO TYR ALA ARG GLY ALA THR THR LEU ASP MET SEQRES 19 B 313 LYS GLY VAL LEU ASN GLU LEU GLU GLU LYS ARG PRO GLY SEQRES 20 B 313 THR LYS PHE ASN PHE VAL ARG GLY TYR LEU LYS LYS LYS SEQRES 21 B 313 LYS LEU PHE GLU PRO GLU ILE LYS GLU LYS GLU ILE LYS SEQRES 22 B 313 GLU CYS LYS ILE CYS ARG MET PRO SER SER GLY ASP ILE SEQRES 23 B 313 CYS ALA PHE CYS LYS PHE TRP GLY LEU LYS LYS GLU ILE SEQRES 24 B 313 ASN PHE LYS VAL SER SER THR ASP GLU GLU PRO PHE GLY SEQRES 25 B 313 PRO HET AMP A 401 23 HET ZN A 402 1 HET ZN A 403 1 HET FES A 404 4 HET AMP B 401 23 HET ZN B 402 1 HET ZN B 403 1 HET FES B 404 4 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 3 AMP 2(C10 H14 N5 O7 P) FORMUL 4 ZN 4(ZN 2+) FORMUL 6 FES 2(FE2 S2) FORMUL 11 HOH *57(H2 O) HELIX 1 AA1 CYS A 22 TYR A 41 1 20 HELIX 2 AA2 GLY A 57 LEU A 70 1 14 HELIX 3 AA3 TYR A 86 GLY A 102 1 17 HELIX 4 AA4 ILE A 110 LEU A 114 1 5 HELIX 5 AA5 CYS A 128 ASN A 146 1 19 HELIX 6 AA6 ASN A 156 HIS A 170 1 15 HELIX 7 AA7 ASN A 172 LYS A 178 1 7 HELIX 8 AA8 THR A 200 GLY A 212 1 13 HELIX 9 AA9 ALA A 226 ARG A 242 1 17 HELIX 10 AB1 GLY A 244 LYS A 257 1 14 HELIX 11 AB2 LYS A 258 ILE A 264 5 7 HELIX 12 AB3 CYS A 284 GLY A 291 1 8 HELIX 13 AB4 CYS B 22 TYR B 41 1 20 HELIX 14 AB5 GLY B 57 LEU B 70 1 14 HELIX 15 AB6 TYR B 86 GLY B 102 1 17 HELIX 16 AB7 ILE B 110 LEU B 114 1 5 HELIX 17 AB8 CYS B 128 ASN B 146 1 19 HELIX 18 AB9 ASN B 156 HIS B 170 1 15 HELIX 19 AC1 ASN B 172 LYS B 178 1 7 HELIX 20 AC2 THR B 200 GLY B 212 1 13 HELIX 21 AC3 ALA B 226 ARG B 242 1 17 HELIX 22 AC4 GLY B 244 LYS B 257 1 14 HELIX 23 AC5 LYS B 258 ILE B 264 5 7 HELIX 24 AC6 CYS B 284 GLY B 291 1 8 SHEET 1 AA1 2 ILE A 12 ILE A 14 0 SHEET 2 AA1 2 MET A 19 LEU A 21 -1 O MET A 19 N ILE A 14 SHEET 1 AA2 6 LEU A 105 ARG A 109 0 SHEET 2 AA2 6 ASN A 73 ASN A 80 1 N CYS A 76 O HIS A 106 SHEET 3 AA2 6 ARG A 49 ALA A 53 1 N ILE A 50 O ASN A 73 SHEET 4 AA2 6 ALA A 150 ALA A 152 1 O ALA A 150 N LEU A 51 SHEET 5 AA2 6 LYS A 191 VAL A 193 1 O LYS A 191 N ILE A 151 SHEET 6 AA2 6 ILE A 182 LEU A 183 -1 N LEU A 183 O LYS A 192 SHEET 1 AA3 2 LYS A 270 GLU A 271 0 SHEET 2 AA3 2 PRO A 278 SER A 279 -1 O SER A 279 N LYS A 270 SHEET 1 AA4 2 ILE B 12 ILE B 14 0 SHEET 2 AA4 2 MET B 19 LEU B 21 -1 O MET B 19 N ILE B 14 SHEET 1 AA5 6 LEU B 105 ARG B 109 0 SHEET 2 AA5 6 ASN B 73 ASN B 80 1 N CYS B 76 O HIS B 106 SHEET 3 AA5 6 ARG B 49 ALA B 53 1 N ILE B 50 O ASN B 73 SHEET 4 AA5 6 ALA B 150 ALA B 152 1 O ALA B 150 N LEU B 51 SHEET 5 AA5 6 LYS B 191 VAL B 193 1 O LYS B 191 N ILE B 151 SHEET 6 AA5 6 ILE B 182 LEU B 183 -1 N LEU B 183 O LYS B 192 SHEET 1 AA6 2 LYS B 270 GLU B 271 0 SHEET 2 AA6 2 PRO B 278 SER B 279 -1 O SER B 279 N LYS B 270 LINK SG CYS A 3 ZN ZN A 402 1555 1555 2.16 LINK SG CYS A 6 ZN ZN A 402 1555 1555 2.44 LINK SG CYS A 22 ZN ZN A 402 1555 1555 2.52 LINK ND1 HIS A 25 ZN ZN A 402 1555 1555 2.22 LINK SG CYS A 128 FE1 FES A 404 1555 1555 2.48 LINK SG CYS A 131 FE2 FES A 404 1555 1555 2.12 LINK SG CYS A 220 FE1 FES A 404 1555 1555 2.67 LINK SG CYS A 272 ZN ZN A 403 1555 1555 2.26 LINK SG CYS A 275 ZN ZN A 403 1555 1555 2.49 LINK SG CYS A 284 ZN ZN A 403 1555 1555 2.23 LINK SG CYS A 287 ZN ZN A 403 1555 1555 2.73 LINK SG CYS B 3 ZN ZN B 402 1555 1555 2.19 LINK SG CYS B 6 ZN ZN B 402 1555 1555 2.34 LINK SG CYS B 22 ZN ZN B 402 1555 1555 2.52 LINK ND1 HIS B 25 ZN ZN B 402 1555 1555 2.26 LINK SG CYS B 128 FE1 FES B 404 1555 1555 2.62 LINK SG CYS B 131 FE2 FES B 404 1555 1555 2.10 LINK SG CYS B 220 FE1 FES B 404 1555 1555 2.40 LINK SG CYS B 272 ZN ZN B 403 1555 1555 2.31 LINK SG CYS B 275 ZN ZN B 403 1555 1555 2.50 LINK SG CYS B 284 ZN ZN B 403 1555 1555 2.17 LINK SG CYS B 287 ZN ZN B 403 1555 1555 2.76 CISPEP 1 TYR A 16 PRO A 17 0 -0.54 CISPEP 2 TYR B 16 PRO B 17 0 0.22 SITE 1 AC1 12 ALA A 53 VAL A 54 SER A 55 SER A 60 SITE 2 AC1 12 LEU A 77 ILE A 79 LEU A 81 LYS A 135 SITE 3 AC1 12 THR A 153 GLY A 154 HIS A 155 HOH A 510 SITE 1 AC2 4 CYS A 3 CYS A 6 CYS A 22 HIS A 25 SITE 1 AC3 4 CYS A 272 CYS A 275 CYS A 284 CYS A 287 SITE 1 AC4 4 PRO A 127 CYS A 128 CYS A 131 CYS A 220 SITE 1 AC5 10 ALA B 53 VAL B 54 SER B 55 SER B 60 SITE 2 AC5 10 LEU B 77 ILE B 79 LYS B 135 THR B 153 SITE 3 AC5 10 GLY B 154 HIS B 155 SITE 1 AC6 4 CYS B 3 CYS B 6 CYS B 22 HIS B 25 SITE 1 AC7 4 CYS B 272 CYS B 275 CYS B 284 CYS B 287 SITE 1 AC8 3 CYS B 128 CYS B 131 CYS B 220 CRYST1 68.860 72.320 128.280 90.00 90.00 90.00 P 21 21 21 8 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 0.014522 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007795 0.00000