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Yorodumi- PDB-6ato: Crystal structure of hGSTA1-1 complexed with GSH and MPD in each ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ato | ||||||
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Title | Crystal structure of hGSTA1-1 complexed with GSH and MPD in each subunit | ||||||
Components | Glutathione S-transferase A1 | ||||||
Keywords | TRANSFERASE / Glutathione S-transferase / glutathione transferase / GST / hGSTA1-1 / GSH | ||||||
Function / homology | Function and homology information Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / epithelial cell differentiation / xenobiotic metabolic process / glutathione metabolic process / fatty acid binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Kumari, V. / Ji, X. | ||||||
Citation | Journal: To be published Title: The dynamic nature of hGSTA1-1 C-terminal helix Authors: Kumari, V. / Ji, X. #1: Journal: J. Mol. Biol. / Year: 1993 Title: Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes. Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ato.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ato.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ato.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ato_validation.pdf.gz | 971.9 KB | Display | wwPDB validaton report |
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Full document | 6ato_full_validation.pdf.gz | 990.5 KB | Display | |
Data in XML | 6ato_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 6ato_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6ato ftp://data.pdbj.org/pub/pdb/validation_reports/at/6ato | HTTPS FTP |
-Related structure data
Related structure data | 6atpC 6atqC 1guhS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25538.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pET30b(+)/hGSTA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: 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: 2.23 Å3/Da / Density % sol: 44.89 % / Description: Rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 200 MME, 25% (w/v), 0.1 M Tris HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 63121 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.22 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.15 / Num. unique all: 5935 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GUH Resolution: 1.55→28.976 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→28.976 Å
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Refine LS restraints |
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LS refinement shell |
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