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Open data
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Basic information
Entry | Database: PDB / ID: 5z9f | ||||||
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Title | Bacterial GyrB ATPase domain in complex with a chemical fragment | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | ISOMERASE / DNA Topoisomerase / Antibacterial / Drug Target / Fragment-base Lead Discovery | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, X. / Zhou, H. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.2 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z4hC ![]() 5z4oC ![]() 5z9bC ![]() 5z9eC ![]() 5z9lC ![]() 5z9mC ![]() 5z9nC ![]() 5z9pC ![]() 5z9qC ![]() 4duhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22705.473 Da / Num. of mol.: 2 / Fragment: UNP residues 15-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 Gene: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-AX7 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 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: 1.76→56.66 Å / Num. obs: 39564 / % possible obs: 91.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 52 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 14 / Num. unique obs: 4239 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DUH Resolution: 1.76→56.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.261 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.418 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→56.66 Å
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Refine LS restraints |
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