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Yorodumi- PDB-6f71: Crystal structure of glutathione transferase Omega 6S from Tramet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f71 | |||||||||
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Title | Crystal structure of glutathione transferase Omega 6S from Trametes versicolor in complex with naringenin | |||||||||
Components | glutathione transferaseGlutathione S-transferase | |||||||||
Keywords | TRANSFERASE / Glutathione / fungi / polyphenols / wood decayers | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Trametes versicolor (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å | |||||||||
Authors | Schwartz, M. / Favier, F. / Didierjean, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Sci Rep / Year: 2018 Title: Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor. Authors: Schwartz, M. / Perrot, T. / Aubert, E. / Dumarcay, S. / Favier, F. / Gerardin, P. / Morel-Rouhier, M. / Mulliert, G. / Saiag, F. / Didierjean, C. / Gelhaye, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f71.cif.gz | 363.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f71.ent.gz | 301.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/6f71 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f71 | HTTPS FTP |
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-Related structure data
Related structure data | 6f43C 6f4bC 6f4fC 6f4kC 6f51C 6f66C 6f67C 6f68C 6f69C 6f6aC 6f70SC 6ht6C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27816.197 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes versicolor (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E158*PLUS #2: Chemical | ChemComp-CWE / #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: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 25 % PEG 1500, 0.1 M MMT pH 6.5 buffer (containing DL-malic acid, MES and Tris base in the molar ratios 1:2:2, respectively) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.35 Å / Num. obs: 46447 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.3→2.36 Å / Rmerge(I) obs: 0.599 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F70 Resolution: 2.301→45.872 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.65 / 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: 2.301→45.872 Å
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Refine LS restraints |
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LS refinement shell |
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