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Yorodumi- PDB-3qag: Human Glutathione Transferase O2 with glutathione -new crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qag | ||||||
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Title | Human Glutathione Transferase O2 with glutathione -new crystal form | ||||||
Components | Glutathione S-transferase omega-2 | ||||||
Keywords | TRANSFERASE / Glutathione Transferase / GST / Dehydroascorbate Reductase / Reductase | ||||||
Function / homology | Function and homology information methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / cellular response to arsenic-containing substance / Glutathione conjugation / glutathione transferase / glutathione transferase activity ...methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / cellular response to arsenic-containing substance / Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / oxidoreductase activity / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhou, H. / Board, P.G. / Oakley, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases. Authors: Zhou, H. / Brock, J. / Liu, D. / Board, P.G. / Oakley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qag.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qag.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/3qag ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qag | HTTPS FTP |
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-Related structure data
Related structure data | 3q18SC 3q19C 3vlnC 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: 27769.898 Da / Num. of mol.: 1 / Mutation: C80S, C121S, C136S, C140S, C170S, C214S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/rep4 / References: UniProt: Q9H4Y5, glutathione transferase | ||||
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#2: Chemical | ChemComp-GSH / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-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: 52.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes pH7.5, 2% v/v Polyethylene glycol 400, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954448 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Monochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954448 Å / Relative weight: 1 |
Reflection | Resolution: 2→12 Å / Num. all: 19843 / Num. obs: 19843 / % possible obs: 98.6 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1428 / % possible all: 99.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q18 Resolution: 2→12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.005 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.403 Å2
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Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.395 Å / Origin y: 21.746 Å / Origin z: 14.2163 Å
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Refinement TLS group |
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