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Yorodumi- PDB-6gav: Extremely 'open' clamp structure of DNA gyrase: role of the Coryn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gav | ||||||
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Title | Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert | ||||||
Components | DNA gyrase subunit B,DNA gyrase subunit A | ||||||
Keywords | DNA BINDING 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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion 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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Petrella, S. / Capton, E. / Alzari, P.M. / Aubry, A. / MAyer, C. | ||||||
Citation | Journal: Structure / Year: 2019 Title: Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity. Authors: Petrella, S. / Capton, E. / Raynal, B. / Giffard, C. / Thureau, A. / Bonnete, F. / Alzari, P.M. / Aubry, A. / Mayer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gav.cif.gz | 880.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gav.ent.gz | 733 KB | Display | PDB format |
PDBx/mmJSON format | 6gav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gav_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 6gav_full_validation.pdf.gz | 484.3 KB | Display | |
Data in XML | 6gav_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 6gav_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/6gav ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6gav | HTTPS FTP |
-Related structure data
Related structure data | 6gauC 3ifzS 3ig0S 3zkdS 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: 130449.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gyrB, gyrA, Rv0006, MTCY10H4.04 / Production host: Escherichia coli (E. coli) / References: UniProt: F6N7X0, UniProt: P9WG47, EC: 5.99.1.3 #2: Chemical | ChemComp-MES / #3: 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: 3.02 Å3/Da / Density % sol: 59.25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 100 mM Sodium Acetate 100 mM MES pH 6.5 26% PEG 400 25% EG 10 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.15 Å / Num. obs: 94824 / % possible obs: 99.2 % / Redundancy: 3.38 % / Biso Wilson estimate: 74.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.9 |
Reflection shell | Highest resolution: 2.6 Å / Rmerge(I) obs: 1.253 / CC1/2: 0.531 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IFZ 3IG0 3ZKD Resolution: 2.6→46.15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.269
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Displacement parameters | Biso max: 235.61 Å2 / Biso mean: 94.53 Å2 / Biso min: 20 Å2
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Refine analyze | Luzzati coordinate error obs: 0.405 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→46.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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