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Yorodumi- PDB-2r6k: Crystal structure of an I71V hGSTA1-1 mutant in complex with S-he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r6k | ||||||
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Title | Crystal structure of an I71V hGSTA1-1 mutant in complex with S-hexylglutathione | ||||||
Components | Glutathione S-transferase A1 | ||||||
Keywords | TRANSFERASE / human Alpha class glutathione transferase 1-1 / s-hexyl-glutathione / X-ray crystal structure | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å | ||||||
Authors | Dirr, H.W. / Fisher, L. / Burke, J.P.W.G. / Sayed, M. / Sewell, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: The role of a topologically conserved isoleucine in glutathione transferase structure, stability and function. Authors: Achilonu, I. / Gildenhuys, S. / Fisher, L. / Burke, J. / Fanucchi, S. / Sewell, B.T. / Fernandes, M. / Dirr, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r6k.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r6k.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 2r6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r6k_validation.pdf.gz | 896.1 KB | Display | wwPDB validaton report |
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Full document | 2r6k_full_validation.pdf.gz | 905.7 KB | Display | |
Data in XML | 2r6k_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2r6k_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r6k ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r6k | HTTPS FTP |
-Related structure data
Related structure data | 3ktlC 1k3lS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 4 - 222 / Label seq-ID: 4 - 222
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-Components
#1: Protein | Mass: 25656.094 Da / Num. of mol.: 2 / Mutation: I71V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pKHA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase #2: Chemical | #3: 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: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14 mg protein per ml, 0.1M Tris-HCl, 10 mM DTT, 19% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2005 |
Radiation | Monochromator: Nickel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→20.091 Å / Num. all: 20428 / Num. obs: 14904 |
Reflection shell | Highest resolution: 2.51 Å |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K3L.pdb Resolution: 2.51→20.09 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.822 / SU B: 12.179 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.008 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→20.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1781 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.51→2.574 Å / Total num. of bins used: 20
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