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- PDB-6kzv: Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kzv | ||||||
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Title | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | ISOMERASE / Inhibitor / Complex / Topoisomerase / Escherichia coli | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mima, M. / Ushiyama, F. | ||||||
![]() | ![]() Title: Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. Authors: Ushiyama, F. / Amada, H. / Takeuchi, T. / Tanaka-Yamamoto, N. / Kanazawa, H. / Nakano, K. / Mima, M. / Masuko, A. / Takata, I. / Hitaka, K. / Iwamoto, K. / Sugiyama, H. / Ohtake, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.6 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kzxC ![]() 6kzzC ![]() 6l01C ![]() 1aj6S 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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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.) ![]() ![]() ![]() ![]() References: UniProt: A0A4V5JMQ9, UniProt: P0AES6*PLUS, DNA topoisomerase (ATP-hydrolysing) |
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#2: Chemical | ChemComp-E0F / ~{ |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: MES, Magnesium chloride, PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→18.9 Å / Num. obs: 7467 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 733 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AJ6 Resolution: 2.4→18.9 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.4→18.9 Å
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LS refinement shell | Resolution: 2.4→2.463 Å / Rfactor Rfree: 0.417 / Rfactor Rwork: 0.233 |