+Open data
-Basic information
Entry | Database: PDB / ID: 4ddu | ||||||
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Title | Thermotoga maritima reverse gyrase, C2 FORM 1 | ||||||
Components | Reverse gyrase | ||||||
Keywords | HYDROLASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE | ||||||
Function / homology | Function and homology information Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / reverse gyrase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / helicase activity / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Rudolph, M.G. / Klostermeier, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling. Authors: Rudolph, M.G. / Del Toro Duany, Y. / Jungblut, S.P. / Ganguly, A. / Klostermeier, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ddu.cif.gz | 467.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ddu.ent.gz | 384.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ddu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/4ddu ftp://data.pdbj.org/pub/pdb/validation_reports/dd/4ddu | HTTPS FTP |
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-Related structure data
Related structure data | 4ddtSC 4ddvC 4ddwC 4ddxC 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: 128478.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rgy, topR, TM_0173 / Production host: Escherichia coli (E. coli) / References: UniProt: O51934, DNA helicase, EC: 5.99.1.3 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M MgCl2, 0.1M HEPES/NaOH pH7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.27832 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27832 Å / Relative weight: 1 |
Reflection | Resolution: 3→44.9 Å / Num. obs: 24946 / % possible obs: 99.8 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.2744 / Rsym value: 0.2744 / Net I/σ(I): 7.09 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 13.52 % / Rmerge(I) obs: 0.9414 / Mean I/σ(I) obs: 1.11 / Rsym value: 0.9414 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4DDT Resolution: 3→44.223 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.406 Å2 / ksol: 0.298 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→44.223 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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