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Yorodumi- PDB-8ax1: Crystal structure of Trametes versicolor glutathione transferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ax1 | ||||||
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Title | Crystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with hydroxy-tetranitro-nitrosyl-ruthenate | ||||||
Components | Glutathione transferase | ||||||
Keywords | TRANSFERASE / glutathione transferase / GSTO / detoxification | ||||||
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: 1.65 Å | ||||||
Authors | Schwartz, M. / Didierjean, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structural insights into the interactions of glutathione transferases with a nitric oxide carrier and sodium nitroprusside. Authors: Schwartz, M. / Perrot, T. / Beurton, J. / Zannini, F. / Morel-Rouhier, M. / Gelhaye, E. / Neiers, F. / Schaniel, D. / Favier, F. / Jacquot, J.P. / Leroy, P. / Clarot, I. / Boudier, A. / Didierjean, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ax1.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ax1.ent.gz | 159.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ax1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ax1_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8ax1_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8ax1_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 8ax1_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/8ax1 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/8ax1 | HTTPS FTP |
-Related structure data
Related structure data | 8awzC 8ax0C 8ax2C 6f43S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, glutathione transferase |
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-Non-polymers , 6 types, 409 molecules
#2: Chemical | ChemComp-ODU / #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | ChemComp-RU / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.66 Å3/Da / Density % sol: 53.68 % |
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Crystal grow | Temperature: 277 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 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9814 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9814 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→47.09 Å / Num. obs: 69693 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.073 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 5091 / CC1/2: 0.74 / Rrim(I) all: 0.884 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F43 Resolution: 1.65→28.71 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.42 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.21 Å2 / Biso mean: 25.3183 Å2 / Biso min: 10.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→28.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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