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- PDB-6f8j: Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(et... -

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Basic information

Entry
Database: PDB / ID: 6f8j
TitleCrystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-(1H-pyrazol-1-yl)-N-(pyridin-3-yl)pyridine-3-carboxamide
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Binding Sites / DNA Gyrase / inhibitors / pyridine-3-carboxamides / topoisomerase IV
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CZ5 / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsNarramore, S.K. / Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A. / Fishwick, C.W.G.
CitationJournal: Bioorg.Med.Chem. / Year: 2019
Title: New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.
Authors: Narramore, S. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M. / Fishwick, C.W.G.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6302
Polymers24,2781
Non-polymers3511
Water1,72996
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.790, 99.790, 50.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA gyrase subunit B


Mass: 24278.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AES7, UniProt: P0AES6*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-CZ5 / 6-(ethylcarbamoylamino)-4-pyrazol-1-yl-~{N}-pyridin-3-yl-pyridine-3-carboxamide


Mass: 351.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25-30% PEG400 and 100 mM Hepes pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→49.9 Å / Num. obs: 21281 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.068 / Rrim(I) all: 0.214 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-29.51.56815610.4680.5331.65999.2
8.72-49.98.20.1422740.9880.0510.15199.7

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6F86

6f86


Resolution: 1.95→49.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.278 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 967 4.5 %RANDOM
Rwork0.1988 ---
obs0.2002 20298 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.48 Å2 / Biso mean: 34.356 Å2 / Biso min: 20.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å20 Å2
2---0.51 Å20 Å2
3---1.65 Å2
Refinement stepCycle: final / Resolution: 1.95→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 26 97 1567
Biso mean--28.84 41.94 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191540
X-RAY DIFFRACTIONr_bond_other_d0.0020.021411
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9622090
X-RAY DIFFRACTIONr_angle_other_deg0.9753.0053269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28124.16772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37315259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2141511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021743
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 65 -
Rwork0.289 1490 -
all-1555 -
obs--99.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.12580.1695-0.94249.5665-1.25333.5439-0.1770.2562-0.479-0.1030.14230.27150.8567-0.10150.03470.2501-0.0885-0.01560.1893-0.02830.129766.637323.439442.2111
26.7577-0.4401-3.93023.8779-1.26716.6903-0.1310.0803-0.0460.21450.18370.45930.1129-0.6946-0.05280.0439-0.0314-0.02020.15330.03230.151959.694534.521757.3093
31.50791.1177-1.01941.5244-1.11563.0521-0.06650.0139-0.186-0.25230.0720.20620.4228-0.1219-0.00540.1004-0.048-0.08310.09350.01720.195368.144827.618259.9532
42.28710.3231.25742.19180.26065.526-0.0351-0.0074-0.1595-0.01660.00740.01430.29270.08340.02770.0325-0.01050.00650.02460.0030.045973.979928.884860.1016
57.2151-1.4938-3.98730.54591.88217.52110.14890.53190.0372-0.0728-0.0508-0.01910.0071-0.182-0.09820.1379-0.0732-0.01060.1151-0.01150.027470.494635.381640.2744
68.1762-0.0101-2.35250.7635-1.04974.3282-0.10290.2371-0.1827-0.20960.09890.170.1481-0.15650.0040.0879-0.0098-0.0370.11770.00890.121356.68941.8548.5045
78.43560.5861-1.55921.49320.61894.03870.2322-0.11950.58530.07220.07760.0619-0.4981-0.0152-0.30980.12190.0092-0.02280.05720.02210.173266.141745.721352.7469
87.1907-0.0664-2.11561.49650.2752.92130.0279-0.1686-0.06430.0449-0.04350.0394-0.2253-0.010.01560.12370.0228-0.00990.09180.01280.139958.247649.047454.7111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 38
2X-RAY DIFFRACTION2A39 - 58
3X-RAY DIFFRACTION3A59 - 120
4X-RAY DIFFRACTION4A121 - 173
5X-RAY DIFFRACTION5A174 - 186
6X-RAY DIFFRACTION6A187 - 197
7X-RAY DIFFRACTION7A198 - 212
8X-RAY DIFFRACTION8A213 - 219

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