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Open data
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Basic information
Entry | Database: PDB / ID: 7dqm | ||||||
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Title | E. coli GyrB ATPase domain in complex with Naringenin | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | ISOMERASE | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, Y. / Zhou, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Identification of new building blocks by fragment screening for discovering GyrB inhibitors. Authors: Yu, Y. / Guo, J. / Cai, Z. / Ju, Y. / Xu, J. / Gu, Q. / 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 | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 714.5 KB | Display | ![]() |
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Full document | ![]() | 715.7 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dorC ![]() 7dprC ![]() 7dpsC ![]() 7dqfC ![]() 7dqhC ![]() 7dqiC ![]() 7dqjC ![]() 7dqlC ![]() 7dqsC ![]() 7dquC ![]() 7dqwC ![]() 5z9bS 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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Unit cell |
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Components
#1: Protein | Mass: 22648.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A4S5B230, DNA topoisomerase (ATP-hydrolysing) #2: Chemical | ChemComp-AX7 / | #3: Chemical | #4: Chemical | ChemComp-CWE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→56.58 Å / Num. obs: 41802 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.992 / Net I/σ(I): 25.555 |
Reflection shell | Resolution: 1.78→1.84 Å / Num. unique obs: 4138 / CC1/2: 0.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z9B Resolution: 1.78→56.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.137 / 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: 30.951 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→56.58 Å
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Refine LS restraints |
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