HEADER ISOMERASE 13-DEC-17 6F8J TITLE CRYSTAL STRUCTURE OF E. COLI GYRASEB 24KDA IN COMPLEX WITH 6- TITLE 2 [(ETHYLCARBAMOYL)AMINO]-4-(1H-PYRAZOL-1-YL)-N-(PYRIDIN-3-YL)PYRIDINE- TITLE 3 3-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE SUBUNIT B; COMPND 3 CHAIN: A; COMPND 4 EC: 5.99.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 GENE: GYRB, Z5190, ECS4634; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BINDING SITES, DNA GYRASE, INHIBITORS, PYRIDINE-3-CARBOXAMIDES, KEYWDS 2 TOPOISOMERASE IV, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.K.NARRAMORE,C.E.M.STEVENSON,D.M.LAWSON,A.MAXWELL,C.W.G.FISHWICK REVDAT 4 17-JAN-24 6F8J 1 REMARK REVDAT 3 07-AUG-19 6F8J 1 JRNL REVDAT 2 10-JUL-19 6F8J 1 JRNL REVDAT 1 26-JUN-19 6F8J 0 JRNL AUTH S.NARRAMORE,C.E.M.STEVENSON,A.MAXWELL,D.M.LAWSON, JRNL AUTH 2 C.W.G.FISHWICK JRNL TITL NEW INSIGHTS INTO THE BINDING MODE OF PYRIDINE-3-CARBOXAMIDE JRNL TITL 2 INHIBITORS OF E. COLI DNA GYRASE. JRNL REF BIOORG.MED.CHEM. V. 27 3546 2019 JRNL REFN ESSN 1464-3391 JRNL PMID 31257079 JRNL DOI 10.1016/J.BMC.2019.06.015 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20298 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 967 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1444 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.51000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : 1.65000 REMARK 3 B12 (A**2) : -0.25000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.278 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6F8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 49.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.20300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 1.56800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 6F86 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-30% PEG400 AND 100 MM HEPES PH REMARK 280 6.5., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 33.47333 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 16.73667 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 16.73667 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 33.47333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 SER A 4 REMARK 465 TYR A 5 REMARK 465 ASP A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 ILE A 10 REMARK 465 LYS A 11 REMARK 465 VAL A 12 REMARK 465 LEU A 13 REMARK 465 LYS A 14 REMARK 465 HIS A 99 REMARK 465 ALA A 100 REMARK 465 GLY A 101 REMARK 465 GLY A 102 REMARK 465 LYS A 103 REMARK 465 PHE A 104 REMARK 465 ASP A 105 REMARK 465 ASP A 106 REMARK 465 ASN A 107 REMARK 465 SER A 108 REMARK 465 TYR A 109 REMARK 465 LYS A 110 REMARK 465 VAL A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 GLY A 114 REMARK 465 LEU A 115 REMARK 465 HIS A 116 REMARK 465 GLY A 220 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 ARG A 20 NH1 NH2 REMARK 470 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 57 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 ASN A 178 -58.87 69.62 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 CZ5 A 500 DBREF 6F8J A 1 220 UNP P0AES7 GYRB_ECO57 1 220 SEQADV 6F8J SER A 0 UNP P0AES7 EXPRESSION TAG SEQRES 1 A 221 SER MET SER ASN SER TYR ASP SER SER SER ILE LYS VAL SEQRES 2 A 221 LEU LYS GLY LEU ASP ALA VAL ARG LYS ARG PRO GLY MET SEQRES 3 A 221 TYR ILE GLY ASP THR ASP ASP GLY THR GLY LEU HIS HIS SEQRES 4 A 221 MET VAL PHE GLU VAL VAL ASP ASN ALA ILE ASP GLU ALA SEQRES 5 A 221 LEU ALA GLY HIS CYS LYS GLU ILE ILE VAL THR ILE HIS SEQRES 6 A 221 ALA ASP ASN SER VAL SER VAL GLN ASP ASP GLY ARG GLY SEQRES 7 A 221 ILE PRO THR GLY ILE HIS PRO GLU GLU GLY VAL SER ALA SEQRES 8 A 221 ALA GLU VAL ILE MET THR VAL LEU HIS ALA GLY GLY LYS SEQRES 9 A 221 PHE ASP ASP ASN SER TYR LYS VAL SER GLY GLY LEU HIS SEQRES 10 A 221 GLY VAL GLY VAL SER VAL VAL ASN ALA LEU SER GLN LYS SEQRES 11 A 221 LEU GLU LEU VAL ILE GLN ARG GLU GLY LYS ILE HIS ARG SEQRES 12 A 221 GLN ILE TYR GLU HIS GLY VAL PRO GLN ALA PRO LEU ALA SEQRES 13 A 221 VAL THR GLY GLU THR GLU LYS THR GLY THR MET VAL ARG SEQRES 14 A 221 PHE TRP PRO SER LEU GLU THR PHE THR ASN VAL THR GLU SEQRES 15 A 221 PHE GLU TYR GLU ILE LEU ALA LYS ARG LEU ARG GLU LEU SEQRES 16 A 221 SER PHE LEU ASN SER GLY VAL SER ILE ARG LEU ARG ASP SEQRES 17 A 221 LYS ARG ASP GLY LYS GLU ASP HIS PHE HIS TYR GLU GLY HET CZ5 A 500 26 HETNAM CZ5 6-(ETHYLCARBAMOYLAMINO)-4-PYRAZOL-1-YL-~{N}-PYRIDIN-3- HETNAM 2 CZ5 YL-PYRIDINE-3-CARBOXAMIDE FORMUL 2 CZ5 C17 H17 N7 O2 FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 GLY A 15 ARG A 22 1 8 HELIX 2 AA2 ARG A 22 GLY A 28 1 7 HELIX 3 AA3 GLY A 33 ALA A 53 1 21 HELIX 4 AA4 SER A 89 VAL A 97 1 9 HELIX 5 AA5 GLY A 119 LEU A 126 1 8 HELIX 6 AA6 GLU A 183 ASN A 198 1 16 SHEET 1 AA1 3 VAL A 149 PRO A 150 0 SHEET 2 AA1 3 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 AA1 3 ALA A 155 GLU A 159 -1 O ALA A 155 N ARG A 142 SHEET 1 AA2 8 VAL A 149 PRO A 150 0 SHEET 2 AA2 8 LYS A 139 GLU A 146 -1 N GLU A 146 O VAL A 149 SHEET 3 AA2 8 SER A 127 ARG A 136 -1 N ILE A 134 O HIS A 141 SHEET 4 AA2 8 GLY A 164 PRO A 171 -1 O ARG A 168 N GLU A 131 SHEET 5 AA2 8 VAL A 69 ASP A 73 -1 N VAL A 71 O VAL A 167 SHEET 6 AA2 8 GLU A 58 ILE A 63 -1 N ILE A 60 O GLN A 72 SHEET 7 AA2 8 SER A 202 ASP A 207 1 O ARG A 204 N ILE A 59 SHEET 8 AA2 8 GLU A 213 PHE A 216 -1 O PHE A 216 N ILE A 203 SITE 1 AC1 15 VAL A 43 ASN A 46 GLU A 50 VAL A 71 SITE 2 AC1 15 ASP A 73 ARG A 76 GLY A 77 ILE A 78 SITE 3 AC1 15 PRO A 79 ILE A 94 ARG A 136 THR A 165 SITE 4 AC1 15 LEU A 197 HOH A 608 HOH A 637 CRYST1 99.790 99.790 50.210 90.00 90.00 120.00 P 32 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 0.010021 0.005786 0.000000 0.00000 SCALE2 0.000000 0.011571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019916 0.00000