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Yorodumi- PDB-5z9n: S.aureus GyrB ATPase domain in complex with 4,6-dichloro-2-(methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z9n | ||||||
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Title | S.aureus GyrB ATPase domain in complex with 4,6-dichloro-2-(methylthio)pyrimidine | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | ISOMERASE / DNA Topoisomerase / Antibacterial / Drug Target / Fragment-base Lead Discovery | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Huang, X. / Zhou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Medchemcomm / Year: 2018 Title: Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes Authors: Huang, X. / Guo, J. / Liu, Q. / Gu, Q. / Xu, J. / Zhou, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z9n.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z9n.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 5z9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z9n_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 5z9n_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 5z9n_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5z9n_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z9n ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z9n | HTTPS FTP |
-Related structure data
Related structure data | 5z4hC 5z4oC 5z9bC 5z9eC 5z9fC 5z9lC 5z9mC 5z9pC 5z9qC 4duhS 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
#1: Protein | Mass: 22705.473 Da / Num. of mol.: 1 / Fragment: UNP residues 15-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 Gene: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 Production host: Escherichia coli (E. coli) / References: UniProt: P0AES6, EC: 5.99.1.3 | ||
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#2: Chemical | ChemComp-HX5 / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M MES pH 6.0, 2.5M MgSO4, 8mM Tris-(2-carboxyethyl)phosphine (TECP) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→97.69 Å / Num. obs: 9100 / % possible obs: 99.9 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 10.6 / Num. unique obs: 876 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DUH Resolution: 2.54→69.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.337 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 35.25 Å2
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Refinement step | Cycle: 1 / Resolution: 2.54→69.17 Å
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