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Yorodumi- PDB-3zfb: Crystal structure of the I75A mutant of human class alpha glutath... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zfb | ||||||
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Title | Crystal structure of the I75A mutant of human class alpha glutathione transferase in the apo form | ||||||
Components | GLUTATHIONE S-TRANSFERASE A1 | ||||||
Keywords | TRANSFERASE / XENOBIOTIC DETOXIFICATION / THIOREDOXIN / TOPOLOGICALLY CONSERVED | ||||||
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 / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Parbhoo, N. / Fanucchi, S. / Achilonu, I.A. / Fernandes, M.A. / Gildenhuys, S. / Dirr, H.W. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the I75A Mutant of Human Class Alpha Glutathione Transferase in the Apo Form Authors: Parbhoo, N. / Achilonu, I.A. / Fanucchi, S. / Fernandes, M.A. / Gildenhuys, S. / 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 | 3zfb.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zfb.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 3zfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/3zfb ftp://data.pdbj.org/pub/pdb/validation_reports/zf/3zfb | HTTPS FTP |
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-Related structure data
Related structure data | 1k3lS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25628.041 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PKHA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P08263, glutathione transferase #2: 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: 2.25 Å3/Da / Density % sol: 45.43 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M TRIS, 17% PEG 4000, 2 MM DTT, 0.02% AZIDE, PH 7.5, VAPOUR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 106 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418 |
Detector | Type: BRUKER / Date: Nov 23, 2012 |
Radiation | Monochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→20.5 Å / Num. obs: 107258 / % possible obs: 99.4 % / Observed criterion σ(I): 4.06 / Redundancy: 15.91 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 1454 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 6.98 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.59 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K3L Resolution: 1.86→51.18 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.882 / SU B: 4.842 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGION, HELIX 9 (RESIDUES 209-222) WERE OMITTED FROM THE STRUCTURE.
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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: 23.211 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→51.18 Å
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Refine LS restraints |
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