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Yorodumi- PDB-3mak: Crystal structure of Glutathione transferase dmGSTD1 from Drosoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mak | ||||||
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Title | Crystal structure of Glutathione transferase dmGSTD1 from Drosophila melanogaster, in complex with glutathione | ||||||
Components | Glutathione S-transferase 1-1 | ||||||
Keywords | TRANSFERASE / PROTEIN-SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information DDT-dehydrochlorinase / DDT-dehydrochlorinase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wongsantichon, J. / Robinson, R.C. / Ketterman, A.J. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2012 Title: Structural evidence for conformational changes of Delta class glutathione transferases after ligand binding Authors: Wongsantichon, J. / Robinson, R.C. / Ketterman, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mak.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mak.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3mak ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3mak | HTTPS FTP |
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-Related structure data
Related structure data | 3f6fSC 3g7iC 3gh6C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23892.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GSTD1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P20432, glutathione transferase |
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#2: Chemical | ChemComp-GSH / |
#3: 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: 1.97 Å3/Da / Density % sol: 37.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 25% (w/v) PEG 4000, 0.2M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→20 Å / Num. obs: 16992 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.029 / Χ2: 1.061 / Net I/σ(I): 47.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F6F Resolution: 1.8→18.26 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.37 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.36 Å2 / Biso mean: 15.023 Å2 / Biso min: 3.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→18.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.796→1.843 Å / Total num. of bins used: 20
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