+Open data
-Basic information
Entry | Database: PDB / ID: 3oiy | ||||||
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Title | Helicase domain of reverse gyrase from Thermotoga maritima | ||||||
Components | reverse gyrase helicase domain | ||||||
Keywords | ISOMERASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE | ||||||
Function / homology | P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PYROPHOSPHATE 2- Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Rudolph, M.G. / Klostermeier, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling. Authors: Ganguly, A. / Del Toro Duany, Y. / Rudolph, M.G. / Klostermeier, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oiy.cif.gz | 345.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oiy.ent.gz | 283.5 KB | Display | PDB format |
PDBx/mmJSON format | 3oiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/3oiy ftp://data.pdbj.org/pub/pdb/validation_reports/oi/3oiy | HTTPS FTP |
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-Related structure data
Related structure data | 1gkuS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 48161.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-POP / | #3: Chemical | ChemComp-CL / | #4: 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: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Details: 0.2 M Magnesium formiate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→132.71 Å / Num. obs: 42547 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.35→2.44 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.34 / Rsym value: 0.659 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GKU Resolution: 2.35→44.358 Å / SU ML: 0.38 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.82 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.35→44.358 Å
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Refine LS restraints |
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LS refinement shell |
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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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