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Yorodumi- PDB-5kej: Crystallographic structure of the Tau class glutathione S-transfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kej | ||||||
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Title | Crystallographic structure of the Tau class glutathione S-transferase MiGSTU in complex with S-hexyl-glutathione | ||||||
Components | Tau class glutathione S-transferase | ||||||
Keywords | TRANSFERASE / detoxification | ||||||
Function / homology | Function and homology information toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Mangifera indica (mango) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Valenzuela-Chavira, I. / Serrano-Posada, H. / Lopez-Zavala, A. / Hernandez-Paredes, J. / Sotelo-Mundo, R. | ||||||
Citation | Journal: Biochimie / Year: 2017 Title: Insights into ligand binding to a glutathione S-transferase from mango: Structure, thermodynamics and kinetics. Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / ...Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / Stojanoff, V. / Sotelo-Mundo, R.R. / Islas-Osuna, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kej.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kej.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/5kej ftp://data.pdbj.org/pub/pdb/validation_reports/ke/5kej | HTTPS FTP |
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-Related structure data
Related structure data | 5g5eC 5g5fC 1gwcS 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: 25550.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mangifera indica (mango) / Plasmid: pJExpress404 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 References: UniProt: A0A1P8NWC2*PLUS, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-PEG / #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: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 289 K / Method: batch mode / pH: 6 Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 6.0, 25%(w/v) polyethylene glycol 3350, 5 mM S-hexyl-glutathione |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.181 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40.343 Å / Num. obs: 23652 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on the structure of wheat Tau class glutathione S-transferase (PDB entry 1GWC). Resolution: 2.35→40.343 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.69 Å2 / Biso mean: 43.4792 Å2 / Biso min: 21.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→40.343 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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