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Yorodumi- PDB-6ht6: Crystal structure of glutathione transferase Omega 2S from Tramet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ht6 | ||||||
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Title | Crystal structure of glutathione transferase Omega 2S from Trametes versicolor in complex with 2,4-dihydroxybenzophenone | ||||||
Components | Glutathione S-transferase omega 2S | ||||||
Keywords | TRANSFERASE / glutathione transferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trametes versicolor (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.671 Å | ||||||
Authors | Schwartz, M. / Favier, F. / Didierjean, C. | ||||||
Funding support | France, 1items
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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 | 6ht6.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ht6.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ht6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ht6_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 6ht6_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 6ht6_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6ht6_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/6ht6 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/6ht6 | HTTPS FTP |
-Related structure data
Related structure data | 6f43C 6f4bC 6f4fC 6f4kC 6f51C 6f66C 6f67C 6f68C 6f69C 6f6aC 6f70C 6f71C 6gibS 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: 27328.105 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: A0A452CSY5*PLUS #2: Chemical | #3: Chemical | ChemComp-MG / | #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: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 10.7% PEG4000, 0.1 M pH 7.0 HEPES-MES buffer (in the ratio 4:6, respectively), 0.05 M sodium acetate and 0.05 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→47.774 Å / Num. obs: 15526 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.055 / Rrim(I) all: 0.148 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.67→2.8 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.2 / Rpim(I) all: 0.245 / Rrim(I) all: 0.666 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GIB Resolution: 2.671→47.774 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.23 / 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: 2.671→47.774 Å
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Refine LS restraints |
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LS refinement shell |
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