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Yorodumi- PDB-6f6a: Crystal structure of glutathione transferase Omega 3S from Tramet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f6a | |||||||||
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Title | Crystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with dihydrowogonin from wild-cherry extract | |||||||||
Components | glutathione transferase | |||||||||
Keywords | TRANSFERASE / Glutathione / fungi / polyphenols / wood decayers | |||||||||
Function / homology | Function and homology information glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Trametes versicolor (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 6f6a.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f6a.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 6f6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f6a_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6f6a_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6f6a_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6f6a_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f6a ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f6a | HTTPS FTP |
-Related structure data
Related structure data | 6f43SC 6f4bC 6f4fC 6f4kC 6f51C 6f66C 6f67C 6f68C 6f69C 6f70C 6f71C 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27526.504 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: A0A384E145*PLUS |
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-Non-polymers , 7 types, 316 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-CA / | #8: 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: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 278 K / Method: microbatch Details: 30 % PEG 400 0.2 M calcium acetate 0.1 M acetate buffer, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.97 Å / Num. obs: 63676 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.7→1.74 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F43 Resolution: 1.7→45.483 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.34 / 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: 1.7→45.483 Å
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Refine LS restraints |
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LS refinement shell |
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