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Yorodumi- PDB-6atq: Crystal structure of apo-hGSTA1-1 exhibiting a new conformation o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6atq | ||||||
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Title | Crystal structure of apo-hGSTA1-1 exhibiting a new conformation of C-terminal helix | ||||||
Components | Glutathione S-transferase A1 | ||||||
Keywords | TRANSFERASE / Glutathione S-transferase / glutathione transferase / GST / hGSTA1-1 / apo | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2 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 | 6atq.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6atq.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 6atq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6atq_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 6atq_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 6atq_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 6atq_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6atq ftp://data.pdbj.org/pub/pdb/validation_reports/at/6atq | HTTPS FTP |
-Related structure data
Related structure data | 6atoC 6atpC 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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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 | ChemComp-MPD / ( #3: Chemical | ChemComp-MES / | #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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 2000 MME, 25% (w/v), 0.1 M MES, 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 29807 / % possible obs: 96.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.48 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.4 % / Num. unique obs: 2624 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GUH Resolution: 2→34.917 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.917 Å
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Refine LS restraints |
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LS refinement shell |
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