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Yorodumi- PDB-6gcb: Crystal structure of glutathione transferase Xi 3 from Trametes v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gcb | ||||||
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Title | Crystal structure of glutathione transferase Xi 3 from Trametes versicolor in complex with glutathione | ||||||
Components | Glutathione transferase Xi 3 from Trametes versicolor | ||||||
Keywords | TRANSFERASE / glutathione transferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trametes versicolor (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å | ||||||
Authors | Schwartz, M. / Favier, F. / Didierjean, C. | ||||||
Funding support | France, 1items
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Citation | Journal: FEBS Lett. / Year: 2018 Title: Trametes versicolor glutathione transferase Xi 3, a dual Cys-GST with catalytic specificities of both Xi and Omega classes. Authors: Schwartz, M. / Perrot, T. / Deroy, A. / Roret, T. / Morel-Rouhier, M. / Mulliert, G. / Gelhaye, E. / Favier, F. / Didierjean, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gcb.cif.gz | 238.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gcb.ent.gz | 193.6 KB | Display | PDB format |
PDBx/mmJSON format | 6gcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gcb ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gcb | HTTPS FTP |
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-Related structure data
Related structure data | 6gc9C 6gcaSC 6gccC 6htaC 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: 37163.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes versicolor (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3F2YM27*PLUS #2: Chemical | #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: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 20% (w/v) polyethylene glycol 8,000, 0.1M pH 6.5 sodium cacodylate buffer and 0.2M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97972 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97972 Å / Relative weight: 1 |
Reflection | Resolution: 1.795→48.694 Å / Num. obs: 78924 / % possible obs: 98.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 4842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GCA Resolution: 1.795→48.694 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.795→48.694 Å
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Refine LS restraints |
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LS refinement shell |
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