+Open data
-Basic information
Entry | Database: PDB / ID: 7p2n | ||||||||||||||||||
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Title | E.coli GyrB24 with inhibitor LSJ38 (EBL2684) | ||||||||||||||||||
Components | DNA gyrase subunit B | ||||||||||||||||||
Keywords | DNA BINDING PROTEIN / Gyrase / inhibitor / E.coli / complex | ||||||||||||||||||
Function / homology | Function and homology information DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||||||||||||||
Authors | Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A.M. / Henderson, S.R. / Kikelj, D. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P. | ||||||||||||||||||
Funding support | Switzerland, United Kingdom, European Union, Slovenia, 5items
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Citation | Journal: Acs Omega / Year: 2023 Title: Exploring the 5-Substituted 2-Aminobenzothiazole-Based DNA Gyrase B Inhibitors Active against ESKAPE Pathogens. Authors: Sterle, M. / Durcik, M. / Stevenson, C.E.M. / Henderson, S.R. / Szili, P.E. / Czikkely, M. / Lawson, D.M. / Maxwell, A. / Cahard, D. / Kikelj, D. / Zidar, N. / Pal, C. / Masic, L.P. / Ilas, ...Authors: Sterle, M. / Durcik, M. / Stevenson, C.E.M. / Henderson, S.R. / Szili, P.E. / Czikkely, M. / Lawson, D.M. / Maxwell, A. / Cahard, D. / Kikelj, D. / Zidar, N. / Pal, C. / Masic, L.P. / Ilas, J. / Tomasic, T. / Cotman, A.E. / Zega, A. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p2n.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p2n.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 7p2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p2n ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p2n | HTTPS FTP |
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-Related structure data
Related structure data | 1kznS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24191.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 Gene: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0AES6, DNA topoisomerase (ATP-hydrolysing) |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-4R3 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 34% PEG4000,100mMtris pH8,95mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.16→34.5 Å / Num. obs: 67664 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Net I/σ(I): 10.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kzn Resolution: 1.16→33.94 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.746 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.93 Å2 / Biso mean: 18.155 Å2 / Biso min: 7.49 Å2
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Refinement step | Cycle: final / Resolution: 1.16→33.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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