HEADER ISOMERASE 27-JUL-09 3IFZ TITLE CRYSTAL STRUCTURE OF THE FIRST PART OF THE MYCOBACTERIUM TUBERCULOSIS TITLE 2 DNA GYRASE REACTION CORE: THE BREAKAGE AND REUNION DOMAIN AT 2.7 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BREAKAGE AND REUNION DOMAIN (N-TERMINAL DOMAIN); COMPND 5 EC: 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: GYRA, MT0006, MTCY10H4.04, RV0006; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-29A KEYWDS DNA GYRASE, GYRA, BREAKAGE AND REUNION DOMAIN, TYPE II TOPOISOMERASE, KEYWDS 2 TUBERCULOSIS, QUINOLONE BINDING SITE, DNA BINDING SITE, ANTIBIOTIC KEYWDS 3 RESISTANCE, ATP-BINDING, DNA-BINDING, ISOMERASE, NUCLEOTIDE-BINDING, KEYWDS 4 TOPOISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.PITON,A.AUBRY,M.DELARUE,C.MAYER REVDAT 4 01-NOV-23 3IFZ 1 REMARK SEQADV REVDAT 3 01-NOV-17 3IFZ 1 REMARK REVDAT 2 27-OCT-10 3IFZ 1 JRNL REVDAT 1 28-JUL-10 3IFZ 0 JRNL AUTH J.PITON,S.PETRELLA,M.DELARUE,G.ANDRE-LEROUX,V.JARLIER, JRNL AUTH 2 A.AUBRY,C.MAYER JRNL TITL STRUCTURAL INSIGHTS INTO THE QUINOLONE RESISTANCE MECHANISM JRNL TITL 2 OF MYCOBACTERIUM TUBERCULOSIS DNA GYRASE. JRNL REF PLOS ONE V. 5 12245 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20805881 JRNL DOI 10.1371/JOURNAL.PONE.0012245 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.5.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 42396 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2125 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.77 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.19 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3115 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2475 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2970 REMARK 3 BIN R VALUE (WORKING SET) : 0.2443 REMARK 3 BIN FREE R VALUE : 0.3155 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.65 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 145 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7534 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.55131 REMARK 3 B22 (A**2) : 2.35491 REMARK 3 B33 (A**2) : -9.90622 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.59159 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.343 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL 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 : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 7663 ; 2.000 ; NULL REMARK 3 BOND ANGLES : 10338 ; 2.000 ; NULL REMARK 3 TORSION ANGLES : 1603 ; 0.000 ; NULL REMARK 3 TRIGONAL CARBON PLANES : 217 ; 2.000 ; NULL REMARK 3 GENERAL PLANES : 1123 ; 5.000 ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : 7663 ; 20.000 ; NULL REMARK 3 BAD NON-BONDED CONTACTS : 147 ; 5.000 ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL 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 : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.72 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.980000 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS PLUS CHANNEL CUT REMARK 200 CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42396 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.440 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.42 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : 0.75000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1AB4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, MPD, PEG 4000, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 81.95750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.95750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 54.83000 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 LEU A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 265 REMARK 465 ARG A 266 REMARK 465 THR A 267 REMARK 465 SER A 268 REMARK 465 ALA A 500 REMARK 465 ALA A 501 REMARK 465 GLU A 502 REMARK 465 HIS A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 HIS A 506 REMARK 465 HIS A 507 REMARK 465 HIS A 508 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 THR B 4 REMARK 465 THR B 5 REMARK 465 LEU B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 ASP B 9 REMARK 465 ASP B 10 REMARK 465 SER B 11 REMARK 465 LEU B 12 REMARK 465 ASP B 13 REMARK 465 ARG B 14 REMARK 465 ILE B 15 REMARK 465 GLU B 16 REMARK 465 PRO B 17 REMARK 465 VAL B 18 REMARK 465 ASP B 19 REMARK 465 ILE B 20 REMARK 465 GLU B 21 REMARK 465 GLN B 22 REMARK 465 GLU B 23 REMARK 465 MET B 24 REMARK 465 GLN B 25 REMARK 465 ARG B 26 REMARK 465 SER B 27 REMARK 465 TYR B 28 REMARK 465 GLU B 502 REMARK 465 HIS B 503 REMARK 465 HIS B 504 REMARK 465 HIS B 505 REMARK 465 HIS B 506 REMARK 465 HIS B 507 REMARK 465 HIS B 508 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 ILE B 29 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 86 C - N - CA ANGL. DEV. = 10.5 DEGREES REMARK 500 PRO A 472 C - N - CD ANGL. DEV. = -14.6 DEGREES REMARK 500 PRO B 86 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO B 171 C - N - CA ANGL. DEV. = 10.2 DEGREES REMARK 500 PRO B 171 C - N - CD ANGL. DEV. = -13.7 DEGREES REMARK 500 PRO B 472 C - N - CD ANGL. DEV. = -13.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 10 -142.52 56.78 REMARK 500 ASP A 13 3.43 171.87 REMARK 500 ILE A 15 30.38 71.59 REMARK 500 TYR A 84 -32.24 -131.68 REMARK 500 PRO A 86 20.50 -70.34 REMARK 500 ARG A 169 -8.54 -59.28 REMARK 500 PRO A 171 66.84 -63.09 REMARK 500 SER A 178 149.96 -172.14 REMARK 500 ALA A 182 -72.21 -96.06 REMARK 500 ASN A 188 75.60 -158.48 REMARK 500 ASN A 207 58.99 -103.53 REMARK 500 ALA A 210 158.68 -47.91 REMARK 500 ALA A 231 -131.85 45.84 REMARK 500 SER A 263 -4.17 81.40 REMARK 500 ARG A 309 -5.22 91.18 REMARK 500 ASP A 426 68.42 65.99 REMARK 500 TYR B 84 -31.08 -131.19 REMARK 500 PRO B 86 51.09 -57.00 REMARK 500 PRO B 171 62.12 -53.84 REMARK 500 ALA B 182 -161.62 -118.69 REMARK 500 VAL B 183 68.51 -67.39 REMARK 500 ASN B 188 75.63 -158.97 REMARK 500 ASN B 207 58.89 -104.40 REMARK 500 ALA B 210 154.68 -43.86 REMARK 500 ALA B 231 -114.45 73.87 REMARK 500 ARG B 266 -149.79 -111.21 REMARK 500 SER B 307 156.12 173.00 REMARK 500 ARG B 313 91.83 -162.40 REMARK 500 ASP B 426 68.91 65.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AB4 RELATED DB: PDB REMARK 900 59KDA FRAGMENT OF GYRASE A FROM E. COLI DBREF 3IFZ A 1 501 UNP Q07702 GYRA_MYCTU 1 501 DBREF 3IFZ B 1 501 UNP Q07702 GYRA_MYCTU 1 501 SEQADV 3IFZ GLU A 502 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 503 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 504 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 505 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 506 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 507 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS A 508 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ GLU B 502 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 503 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 504 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 505 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 506 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 507 UNP Q07702 EXPRESSION TAG SEQADV 3IFZ HIS B 508 UNP Q07702 EXPRESSION TAG SEQRES 1 A 508 MET THR ASP THR THR LEU PRO PRO ASP ASP SER LEU ASP SEQRES 2 A 508 ARG ILE GLU PRO VAL ASP ILE GLU GLN GLU MET GLN ARG SEQRES 3 A 508 SER TYR ILE ASP TYR ALA MET SER VAL ILE VAL GLY ARG SEQRES 4 A 508 ALA LEU PRO GLU VAL ARG ASP GLY LEU LYS PRO VAL HIS SEQRES 5 A 508 ARG ARG VAL LEU TYR ALA MET PHE ASP SER GLY PHE ARG SEQRES 6 A 508 PRO ASP ARG SER HIS ALA LYS SER ALA ARG SER VAL ALA SEQRES 7 A 508 GLU THR MET GLY ASN TYR HIS PRO HIS GLY ASP ALA SER SEQRES 8 A 508 ILE TYR ASP SER LEU VAL ARG MET ALA GLN PRO TRP SER SEQRES 9 A 508 LEU ARG TYR PRO LEU VAL ASP GLY GLN GLY ASN PHE GLY SEQRES 10 A 508 SER PRO GLY ASN ASP PRO PRO ALA ALA MET ARG TYR THR SEQRES 11 A 508 GLU ALA ARG LEU THR PRO LEU ALA MET GLU MET LEU ARG SEQRES 12 A 508 GLU ILE ASP GLU GLU THR VAL ASP PHE ILE PRO ASN TYR SEQRES 13 A 508 ASP GLY ARG VAL GLN GLU PRO THR VAL LEU PRO SER ARG SEQRES 14 A 508 PHE PRO ASN LEU LEU ALA ASN GLY SER GLY GLY ILE ALA SEQRES 15 A 508 VAL GLY MET ALA THR ASN ILE PRO PRO HIS ASN LEU ARG SEQRES 16 A 508 GLU LEU ALA ASP ALA VAL PHE TRP ALA LEU GLU ASN HIS SEQRES 17 A 508 ASP ALA ASP GLU GLU GLU THR LEU ALA ALA VAL MET GLY SEQRES 18 A 508 ARG VAL LYS GLY PRO ASP PHE PRO THR ALA GLY LEU ILE SEQRES 19 A 508 VAL GLY SER GLN GLY THR ALA ASP ALA TYR LYS THR GLY SEQRES 20 A 508 ARG GLY SER ILE ARG MET ARG GLY VAL VAL GLU VAL GLU SEQRES 21 A 508 GLU ASP SER ARG GLY ARG THR SER LEU VAL ILE THR GLU SEQRES 22 A 508 LEU PRO TYR GLN VAL ASN HIS ASP ASN PHE ILE THR SER SEQRES 23 A 508 ILE ALA GLU GLN VAL ARG ASP GLY LYS LEU ALA GLY ILE SEQRES 24 A 508 SER ASN ILE GLU ASP GLN SER SER ASP ARG VAL GLY LEU SEQRES 25 A 508 ARG ILE VAL ILE GLU ILE LYS ARG ASP ALA VAL ALA LYS SEQRES 26 A 508 VAL VAL ILE ASN ASN LEU TYR LYS HIS THR GLN LEU GLN SEQRES 27 A 508 THR SER PHE GLY ALA ASN MET LEU ALA ILE VAL ASP GLY SEQRES 28 A 508 VAL PRO ARG THR LEU ARG LEU ASP GLN LEU ILE ARG TYR SEQRES 29 A 508 TYR VAL ASP HIS GLN LEU ASP VAL ILE VAL ARG ARG THR SEQRES 30 A 508 THR TYR ARG LEU ARG LYS ALA ASN GLU ARG ALA HIS ILE SEQRES 31 A 508 LEU ARG GLY LEU VAL LYS ALA LEU ASP ALA LEU ASP GLU SEQRES 32 A 508 VAL ILE ALA LEU ILE ARG ALA SER GLU THR VAL ASP ILE SEQRES 33 A 508 ALA ARG ALA GLY LEU ILE GLU LEU LEU ASP ILE ASP GLU SEQRES 34 A 508 ILE GLN ALA GLN ALA ILE LEU ASP MET GLN LEU ARG ARG SEQRES 35 A 508 LEU ALA ALA LEU GLU ARG GLN ARG ILE ILE ASP ASP LEU SEQRES 36 A 508 ALA LYS ILE GLU ALA GLU ILE ALA ASP LEU GLU ASP ILE SEQRES 37 A 508 LEU ALA LYS PRO GLU ARG GLN ARG GLY ILE VAL ARG ASP SEQRES 38 A 508 GLU LEU ALA GLU ILE VAL ASP ARG HIS GLY ASP ASP ARG SEQRES 39 A 508 ARG THR ARG ILE ILE ALA ALA GLU HIS HIS HIS HIS HIS SEQRES 40 A 508 HIS SEQRES 1 B 508 MET THR ASP THR THR LEU PRO PRO ASP ASP SER LEU ASP SEQRES 2 B 508 ARG ILE GLU PRO VAL ASP ILE GLU GLN GLU MET GLN ARG SEQRES 3 B 508 SER TYR ILE ASP TYR ALA MET SER VAL ILE VAL GLY ARG SEQRES 4 B 508 ALA LEU PRO GLU VAL ARG ASP GLY LEU LYS PRO VAL HIS SEQRES 5 B 508 ARG ARG VAL LEU TYR ALA MET PHE ASP SER GLY PHE ARG SEQRES 6 B 508 PRO ASP ARG SER HIS ALA LYS SER ALA ARG SER VAL ALA SEQRES 7 B 508 GLU THR MET GLY ASN TYR HIS PRO HIS GLY ASP ALA SER SEQRES 8 B 508 ILE TYR ASP SER LEU VAL ARG MET ALA GLN PRO TRP SER SEQRES 9 B 508 LEU ARG TYR PRO LEU VAL ASP GLY GLN GLY ASN PHE GLY SEQRES 10 B 508 SER PRO GLY ASN ASP PRO PRO ALA ALA MET ARG TYR THR SEQRES 11 B 508 GLU ALA ARG LEU THR PRO LEU ALA MET GLU MET LEU ARG SEQRES 12 B 508 GLU ILE ASP GLU GLU THR VAL ASP PHE ILE PRO ASN TYR SEQRES 13 B 508 ASP GLY ARG VAL GLN GLU PRO THR VAL LEU PRO SER ARG SEQRES 14 B 508 PHE PRO ASN LEU LEU ALA ASN GLY SER GLY GLY ILE ALA SEQRES 15 B 508 VAL GLY MET ALA THR ASN ILE PRO PRO HIS ASN LEU ARG SEQRES 16 B 508 GLU LEU ALA ASP ALA VAL PHE TRP ALA LEU GLU ASN HIS SEQRES 17 B 508 ASP ALA ASP GLU GLU GLU THR LEU ALA ALA VAL MET GLY SEQRES 18 B 508 ARG VAL LYS GLY PRO ASP PHE PRO THR ALA GLY LEU ILE SEQRES 19 B 508 VAL GLY SER GLN GLY THR ALA ASP ALA TYR LYS THR GLY SEQRES 20 B 508 ARG GLY SER ILE ARG MET ARG GLY VAL VAL GLU VAL GLU SEQRES 21 B 508 GLU ASP SER ARG GLY ARG THR SER LEU VAL ILE THR GLU SEQRES 22 B 508 LEU PRO TYR GLN VAL ASN HIS ASP ASN PHE ILE THR SER SEQRES 23 B 508 ILE ALA GLU GLN VAL ARG ASP GLY LYS LEU ALA GLY ILE SEQRES 24 B 508 SER ASN ILE GLU ASP GLN SER SER ASP ARG VAL GLY LEU SEQRES 25 B 508 ARG ILE VAL ILE GLU ILE LYS ARG ASP ALA VAL ALA LYS SEQRES 26 B 508 VAL VAL ILE ASN ASN LEU TYR LYS HIS THR GLN LEU GLN SEQRES 27 B 508 THR SER PHE GLY ALA ASN MET LEU ALA ILE VAL ASP GLY SEQRES 28 B 508 VAL PRO ARG THR LEU ARG LEU ASP GLN LEU ILE ARG TYR SEQRES 29 B 508 TYR VAL ASP HIS GLN LEU ASP VAL ILE VAL ARG ARG THR SEQRES 30 B 508 THR TYR ARG LEU ARG LYS ALA ASN GLU ARG ALA HIS ILE SEQRES 31 B 508 LEU ARG GLY LEU VAL LYS ALA LEU ASP ALA LEU ASP GLU SEQRES 32 B 508 VAL ILE ALA LEU ILE ARG ALA SER GLU THR VAL ASP ILE SEQRES 33 B 508 ALA ARG ALA GLY LEU ILE GLU LEU LEU ASP ILE ASP GLU SEQRES 34 B 508 ILE GLN ALA GLN ALA ILE LEU ASP MET GLN LEU ARG ARG SEQRES 35 B 508 LEU ALA ALA LEU GLU ARG GLN ARG ILE ILE ASP ASP LEU SEQRES 36 B 508 ALA LYS ILE GLU ALA GLU ILE ALA ASP LEU GLU ASP ILE SEQRES 37 B 508 LEU ALA LYS PRO GLU ARG GLN ARG GLY ILE VAL ARG ASP SEQRES 38 B 508 GLU LEU ALA GLU ILE VAL ASP ARG HIS GLY ASP ASP ARG SEQRES 39 B 508 ARG THR ARG ILE ILE ALA ALA GLU HIS HIS HIS HIS HIS SEQRES 40 B 508 HIS HET MPD A 509 8 HET NA A 510 1 HET MPD B 509 8 HET NA B 510 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM NA SODIUM ION FORMUL 3 MPD 2(C6 H14 O2) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *222(H2 O) HELIX 1 1 GLU A 16 LEU A 41 1 26 HELIX 2 2 LYS A 49 GLY A 63 1 15 HELIX 3 3 SER A 73 TYR A 84 1 12 HELIX 4 4 ASP A 89 MET A 99 1 11 HELIX 5 5 THR A 135 LEU A 142 1 8 HELIX 6 6 PRO A 171 GLY A 177 1 7 HELIX 7 7 ASN A 193 ASN A 207 1 15 HELIX 8 8 ASP A 211 VAL A 223 1 13 HELIX 9 9 SER A 237 GLY A 247 1 11 HELIX 10 10 ASN A 279 ARG A 292 1 14 HELIX 11 11 LYS A 325 THR A 335 1 11 HELIX 12 12 ARG A 357 ALA A 400 1 44 HELIX 13 13 ALA A 400 SER A 411 1 12 HELIX 14 14 THR A 413 ASP A 426 1 14 HELIX 15 15 ASP A 428 MET A 438 1 11 HELIX 16 16 GLN A 439 LEU A 443 5 5 HELIX 17 17 ALA A 444 LYS A 471 1 28 HELIX 18 18 LYS A 471 GLY A 491 1 21 HELIX 19 19 ILE B 29 LEU B 41 1 13 HELIX 20 20 LYS B 49 SER B 62 1 14 HELIX 21 21 SER B 73 TYR B 84 1 12 HELIX 22 22 ALA B 90 MET B 99 1 10 HELIX 23 23 THR B 135 LEU B 142 1 8 HELIX 24 24 PRO B 171 GLY B 177 1 7 HELIX 25 25 ASN B 193 ASN B 207 1 15 HELIX 26 26 ASP B 211 VAL B 223 1 13 HELIX 27 27 SER B 237 GLY B 247 1 11 HELIX 28 28 ASN B 279 ASP B 293 1 15 HELIX 29 29 VAL B 323 THR B 335 1 13 HELIX 30 30 ARG B 357 ALA B 400 1 44 HELIX 31 31 ALA B 400 SER B 411 1 12 HELIX 32 32 THR B 413 ASP B 426 1 14 HELIX 33 33 ASP B 428 MET B 438 1 11 HELIX 34 34 GLN B 439 LEU B 443 5 5 HELIX 35 35 ALA B 444 LYS B 471 1 28 HELIX 36 36 LYS B 471 GLY B 491 1 21 SHEET 1 A 3 ALA A 71 LYS A 72 0 SHEET 2 A 3 GLU A 131 LEU A 134 -1 O ALA A 132 N ALA A 71 SHEET 3 A 3 VAL A 110 GLN A 113 -1 N ASP A 111 O ARG A 133 SHEET 1 B 2 PHE A 152 PRO A 154 0 SHEET 2 B 2 GLN A 161 PRO A 163 -1 O GLU A 162 N ILE A 153 SHEET 1 C 2 SER A 178 ILE A 181 0 SHEET 2 C 2 ALA A 186 ILE A 189 -1 O ILE A 189 N SER A 178 SHEET 1 D 4 GLN A 338 ASN A 344 0 SHEET 2 D 4 ARG A 248 ARG A 254 -1 N ILE A 251 O PHE A 341 SHEET 3 D 4 LEU A 233 VAL A 235 -1 N VAL A 235 O ARG A 252 SHEET 4 D 4 ARG A 497 ILE A 498 1 O ARG A 497 N ILE A 234 SHEET 1 E 4 VAL A 256 VAL A 257 0 SHEET 2 E 4 VAL A 270 GLU A 273 -1 O THR A 272 N VAL A 256 SHEET 3 E 4 ILE A 314 ILE A 318 -1 O ILE A 314 N ILE A 271 SHEET 4 E 4 ILE A 299 ASP A 304 -1 N SER A 300 O GLU A 317 SHEET 1 F 2 LEU A 346 VAL A 349 0 SHEET 2 F 2 VAL A 352 THR A 355 -1 O ARG A 354 N ALA A 347 SHEET 1 G 3 ALA B 71 LYS B 72 0 SHEET 2 G 3 GLU B 131 LEU B 134 -1 O ALA B 132 N ALA B 71 SHEET 3 G 3 VAL B 110 GLN B 113 -1 N ASP B 111 O ARG B 133 SHEET 1 H 2 PHE B 152 PRO B 154 0 SHEET 2 H 2 GLN B 161 PRO B 163 -1 O GLU B 162 N ILE B 153 SHEET 1 I 2 SER B 178 GLY B 180 0 SHEET 2 I 2 THR B 187 ILE B 189 -1 O ILE B 189 N SER B 178 SHEET 1 J 4 GLN B 338 ASN B 344 0 SHEET 2 J 4 ARG B 248 ARG B 254 -1 N ILE B 251 O PHE B 341 SHEET 3 J 4 LEU B 233 VAL B 235 -1 N VAL B 235 O ARG B 252 SHEET 4 J 4 ARG B 497 ILE B 499 1 O ILE B 499 N ILE B 234 SHEET 1 K 4 VAL B 256 GLU B 261 0 SHEET 2 K 4 THR B 267 GLU B 273 -1 O VAL B 270 N GLU B 258 SHEET 3 K 4 ILE B 314 ILE B 318 -1 O ILE B 316 N LEU B 269 SHEET 4 K 4 ILE B 299 ASP B 304 -1 N SER B 300 O GLU B 317 SHEET 1 L 2 LEU B 346 VAL B 349 0 SHEET 2 L 2 VAL B 352 THR B 355 -1 O ARG B 354 N ALA B 347 CISPEP 1 ASP A 262 SER A 263 0 1.81 CISPEP 2 ARG B 264 GLY B 265 0 -1.85 SITE 1 AC1 3 LEU A 105 ASN A 176 SER A 178 SITE 1 AC2 2 LYS A 396 GLN A 431 SITE 1 AC3 6 ARG B 98 LEU B 105 LEU B 109 GLY B 177 SITE 2 AC3 6 SER B 178 HOH B 589 SITE 1 AC4 2 LYS B 396 GLN B 431 CRYST1 163.915 109.660 101.996 90.00 120.40 90.00 C 1 2 1 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 0.006101 0.000000 0.003579 0.00000 SCALE2 0.000000 0.009119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011367 0.00000