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Yorodumi- PDB-6f67: Crystal structure of glutathione transferase Omega 3S from Tramet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f67 | |||||||||
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Title | Crystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with 3,4-Dihydroxybenzophenone | |||||||||
Components | glutathione transferase | |||||||||
Keywords | TRANSFERASE / Glutathione / fungi / polyphenols / wood decayers | |||||||||
Function / homology | Function and homology information glutathione transferase / glutathione transferase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Trametes versicolor (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 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 | 6f67.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f67.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f67_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 6f67_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 6f67_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 6f67_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f67 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f67 | HTTPS FTP |
-Related structure data
Related structure data | 6f43SC 6f4bC 6f4fC 6f4kC 6f51C 6f66C 6f68C 6f69C 6f6aC 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
#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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: 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: 2.61 Å3/Da / Density % sol: 52.92 % |
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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: Jun 23, 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: 2.398→47.23 Å / Num. obs: 22688 / % possible obs: 99.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 1536 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F43 Resolution: 2.398→47.227 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→47.227 Å
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Refine LS restraints |
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LS refinement shell |
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