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Yorodumi- PDB-6k8n: Crystal structure of the Sulfolobus solfataricus topoisomerase III -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k8n | ||||||
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Title | Crystal structure of the Sulfolobus solfataricus topoisomerase III | ||||||
Components | topoisomerase III | ||||||
Keywords | ISOMERASE / DNA BINDING PROTEIN / Topoisomerase III / type IA topoisomerase | ||||||
Function / homology | Function and homology information DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA binding Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, H.Q. / Zhang, J.H. / Zheng, X. / Zheng, Z.F. / Dong, Y.H. / Huang, L. / Gong, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal structures of the Sulfolobus solfataricus topoisomerase III reveal that its C-terminal novel zinc finger part is a unique decatenation domain Authors: Wang, H.Q. / Zhang, J.H. / Zheng, X. / Zheng, Z.F. / Dong, Y.H. / Huang, L. / Gong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k8n.cif.gz | 547.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8n.ent.gz | 451.7 KB | Display | PDB format |
PDBx/mmJSON format | 6k8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8n ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8n | HTTPS FTP |
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-Related structure data
Related structure data | 6k8oC 2gajS 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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Unit cell |
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-Components
#1: Protein | Mass: 76677.344 Da / Num. of mol.: 4 / Mutation: Y318F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZJ8, DNA topoisomerase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 8% (v/v) Tacsimate (pH 4.4), and 13.75% (w/v) Polyethyleneglycerol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 172718 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 35.63 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2 / Num. unique obs: 8284 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GAJ Resolution: 2.1→50 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell |
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