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Yorodumi- PDB-6sra: Crystal structure of glutathione transferase Omega 2C from Tramet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sra | ||||||
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Title | Crystal structure of glutathione transferase Omega 2C from Trametes versicolor in complex with naringenin | ||||||
Components | glutathione transferase | ||||||
Keywords | TRANSFERASE / glutathione transferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trametes versicolor (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å | ||||||
Authors | Schwartz, M. / Favier, F. / Didierjean, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Fungal Genet Biol. / Year: 2021 Title: Diversity of Omega Glutathione Transferases in mushroom-forming fungi revealed by phylogenetic, transcriptomic, biochemical and structural approaches. Authors: Perrot, T. / Schwartz, M. / Deroy, A. / Girardet, J.M. / Kohler, A. / Morel-Rouhier, M. / Favier, F. / Gelhaye, E. / Didierjean, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sra.cif.gz | 185 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sra.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 6sra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/6sra ftp://data.pdbj.org/pub/pdb/validation_reports/sr/6sra | HTTPS FTP |
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-Related structure data
Related structure data | 6hjsC 6sr8SC 6sr9C 6srbC 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: 27428.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trametes versicolor (fungus) / Strain: FP-101664 / Gene: TRAVEDRAFT_67635 / Production host: Escherichia coli (E. coli) / References: UniProt: R7S7J5 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 277 K / Method: microbatch Details: 20% (w/v) polyethylene glycol 4000, 10% (v/v) 2-Propanol and 0.1 M pH 7.5 HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97994 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97994 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.206→37.43 Å / Num. obs: 27025 / % possible obs: 96.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 33.16 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.076 / Rrim(I) all: 0.135 / Net I/σ(I): 5.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SR8 Resolution: 2.206→34.369 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.61 Å2 / Biso mean: 45.1599 Å2 / Biso min: 13.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.206→34.369 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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