+Open data
-Basic information
Entry | Database: PDB / ID: 5iwm | ||||||
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Title | 2.5A structure of GSK945237 with S.aureus DNA gyrase and DNA. | ||||||
Components |
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Keywords | ISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR / fusion protein | ||||||
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 / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding ...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 / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Bax, B.D. / Miles, T.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2016 Title: Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases. Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Jones, G.E. / ...Authors: Miles, T.J. / Hennessy, A.J. / Bax, B. / Brooks, G. / Brown, B.S. / Brown, P. / Cailleau, N. / Chen, D. / Dabbs, S. / Davies, D.T. / Esken, J.M. / Giordano, I. / Hoover, J.L. / Jones, G.E. / Kusalakumari Sukmar, S.K. / Markwell, R.E. / Minthorn, E.A. / Rittenhouse, S. / Gwynn, M.N. / Pearson, N.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iwm.cif.gz | 322.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwm.ent.gz | 255.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iwm_validation.pdf.gz | 924.9 KB | Display | wwPDB validaton report |
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Full document | 5iwm_full_validation.pdf.gz | 938.1 KB | Display | |
Data in XML | 5iwm_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 5iwm_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwm ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwm | HTTPS FTP |
-Related structure data
Related structure data | 5iwiC 2xcsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA gyrase subunit ... , 2 types, 4 molecules BDAC
#1: Protein | Mass: 22605.689 Da / Num. of mol.: 2 Fragment: UNP residues 409-543, 580-644,UNP residues 409-543, 580-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005 / Strain: N315 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3 #2: Protein | Mass: 55521.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3 |
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-DNA chain , 2 types, 2 molecules EF
#3: DNA chain | Mass: 6103.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 6165.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 262 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-6EJ / ( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 13% peg 5000MME, 100mM BisTris, pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9611 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9611 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→25 Å / Num. obs: 65320 / % possible obs: 92.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.6 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2xcs Resolution: 2.5→24.99 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.857 / SU B: 6.332 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.056
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.846 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→24.99 Å
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Refine LS restraints |
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