HEADER ISOMERASE 14-DEC-17 6F96
TITLE CRYSTAL STRUCTURE OF E. COLI GYRASEB 24KDA IN COMPLEX WITH 6-
TITLE 2 [(ETHYLCARBAMOYL)AMINO]-4-[(4-METHOXYPHENYL)AMINO]-N-(PYRIDIN-3-YL)
TITLE 3 PYRIDINE-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 6F96 1 REMARK
REVDAT 3 07-AUG-19 6F96 1 JRNL
REVDAT 2 10-JUL-19 6F96 1 JRNL
REVDAT 1 30-JAN-19 6F96 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. 2.50 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) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.27
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 9812
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) : 0.209
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.238
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 498
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1447
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 72
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.29
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.29000
REMARK 3 B22 (A**2) : 0.29000
REMARK 3 B33 (A**2) : -0.94000
REMARK 3 B12 (A**2) : 0.14000
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): 0.354
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.476
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 6F96 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-17.
REMARK 100 THE DEPOSITION ID IS D_1200007966.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-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 : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : MIRRORS
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10325
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 50.270
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 9.800
REMARK 200 R MERGE (I) : 0.18600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 9.80
REMARK 200 R MERGE FOR SHELL (I) : 1.69100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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 (%): 59.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25-30% PEG 400 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 33.51333
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 16.75667
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 16.75667
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 33.51333
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: MONOMERIC
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: 9180 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 LYS A 21 CE NZ
REMARK 470 ASP A 29 CG OD1 OD2
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 -62.88 63.37
REMARK 500 ASP A 210 11.12 -149.60
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 D0K A 500
DBREF 6F96 A 1 220 UNP P0AES7 GYRB_ECO57 1 220
SEQADV 6F96 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 D0K A 500 30
HETNAM D0K 6-(ETHYLCARBAMOYLAMINO)-4-[(4-METHOXYPHENYL)AMINO]-
HETNAM 2 D0K ~{N}-PYRIDIN-3-YL-PYRIDINE-3-CARBOXAMIDE
FORMUL 2 D0K C21 H22 N6 O3
FORMUL 3 HOH *72(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 GLY A 158 N ILE A 140
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 206 N ILE A 63
SHEET 8 AA2 8 GLU A 213 PHE A 216 -1 O PHE A 216 N ILE A 203
SITE 1 AC1 13 VAL A 43 ASN A 46 GLU A 50 VAL A 71
SITE 2 AC1 13 ASP A 73 ARG A 76 GLY A 77 ILE A 78
SITE 3 AC1 13 PRO A 79 ILE A 94 ARG A 136 LEU A 197
SITE 4 AC1 13 HOH A 601
CRYST1 100.200 100.200 50.270 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 0.009980 0.005762 0.000000 0.00000
SCALE2 0.000000 0.011524 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019893 0.00000