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- PDB-6kzv: Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,... -

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Basic information

Entry
Database: PDB / ID: 6kzv
TitleCrystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Inhibitor / Complex / Topoisomerase / Escherichia coli
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-E0F / : / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMima, M. / Ushiyama, F.
CitationJournal: Acs Omega / Year: 2020
Title: Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.
Authors: Ushiyama, F. / Amada, H. / Takeuchi, T. / Tanaka-Yamamoto, N. / Kanazawa, H. / Nakano, K. / Mima, M. / Masuko, A. / Takata, I. / Hitaka, K. / Iwamoto, K. / Sugiyama, H. / Ohtake, N.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5812
Polymers24,1911
Non-polymers3891
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.444, 53.444, 67.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DNA gyrase subunit B


Mass: 24191.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gyrB, C9Z04_12785 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4V5JMQ9, UniProt: P0AES6*PLUS, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-E0F / ~{N}-[2-[[cyclohexyl(methyl)amino]methyl]phenyl]-2-oxidanylidene-1~{H}-quinoline-3-carboxamide / N-(2-{[cyclohexyl(methyl)amino]methyl}phenyl)-2-oxo-1,2-dihydroquinoline-3-carboxamide


Mass: 389.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MES, Magnesium chloride, PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→18.9 Å / Num. obs: 7467 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 733

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ6

1aj6


Resolution: 2.4→18.9 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.26032 343 -
Rwork0.1955 --
obs0.19859 7120 99.02 %
Refinement stepCycle: LAST / Resolution: 2.4→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 29 21 1587
LS refinement shellResolution: 2.4→2.463 Å / Rfactor Rfree: 0.417 / Rfactor Rwork: 0.233

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