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Yorodumi- PDB-5g5e: Crystallographic structure of the Tau class glutathione S-transfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g5e | ||||||
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Title | Crystallographic structure of the Tau class glutathione S-transferase MiGSTU from mango Mangifera indica L. | ||||||
Components | TAU CLASS GLUTATHIONE S-TRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTATHIONE S-TRANSFERASE / TAU CLASS / MANGO / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 5g5e.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5e.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5e ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5e | HTTPS FTP |
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-Related structure data
Related structure data | 5g5fC 5kejC 1gwcS C: citing same article (ref.) 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: 25550.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MANGIFERA INDICA (mango) Description: THE MIGSTU SEQUENCE WAS IDENTIFIED FROM A MANGO HADEN MESOCARP CDNA SHOTGUN-CDNA SEQUENCING PROJECT. Plasmid: PJEXPRESS404 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A1P8NWC2*PLUS, glutathione transferase | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 6.0, 25%(W/V) POLYETHYLENE GLYCOL 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 / Wavelength: 1.54178 Å |
Detector | Type: BRUKER / Detector: CMOS / Date: May 12, 2015 / Details: HELIOS MX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.3 Å / Num. obs: 20863 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 10.02 Å2 / Rmerge(I) obs: 0.33 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 16.8 / % 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: 1.8→22.312 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→22.312 Å
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Refine LS restraints |
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LS refinement shell |
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