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- PDB-7c7n: Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro... -

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Basic information

Entry
Database: PDB / ID: 7c7n
TitleCrystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-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-, 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
Similarity search - Domain/homology
Chem-FKR / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMima, M. / Ushiyama, F.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors.
Authors: Ushiyama, F. / Amada, H. / Mihara, Y. / Takeuchi, T. / Tanaka-Yamamoto, N. / Mima, M. / Kamitani, M. / Wada, R. / Tamura, Y. / Endo, M. / Masuko, A. / Takata, I. / Hitaka, K. / Sugiyama, H. / Ohtake, N.
History
DepositionMay 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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)24,5472
Polymers24,1911
Non-polymers3551
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.333, 67.052, 68.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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, NCTC10766_01911, NCTC9007_05029 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A210GCC1, UniProt: P0AES6*PLUS, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-FKR / 4-[[6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid


Mass: 355.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M MES pH6.0, 0.2M Ammonium acetate, 24% 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: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→24.49 Å / Num. obs: 8837 / % possible obs: 99.8 % / Redundancy: 5.47 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.278 / Num. unique obs: 861

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ6

1aj6


Resolution: 2.3→24.49 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.072 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27557 439 5 %RANDOM
Rwork0.20602 ---
obs0.20937 8397 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.04 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---0.49 Å20 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 2.3→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 26 37 1600
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 34 -
Rwork0.215 597 -
obs--100 %

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