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Yorodumi- PDB-3gh6: Crystal Structure of Glutathione Transferase dmgstd10 from Drosop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gh6 | ||||||
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Title | Crystal Structure of Glutathione Transferase dmgstd10 from Drosophila melanogaster, in complex with glutathione | ||||||
Components | CG18548-PA (IP02196p) (IP02193p) | ||||||
Keywords | TRANSFERASE / ENZYME-SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information 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: 1.65 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 | 3gh6.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gh6.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/3gh6 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/3gh6 | HTTPS FTP |
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-Related structure data
Related structure data | 3f6fSC 3g7iC 3makC 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: 24622.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line: SL2 cell line / Gene: GstD10, Dmel_CG18548 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9VGA1, 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: 3.42 Å3/Da / Density % sol: 64.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 0.8M sodium dihydrogen phosphate, 0.8M potassium dihydrogen phosphate, 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 315r / Detector: CCD / Date: Nov 20, 2008 |
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: 1.65→20 Å / Num. obs: 40420 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rsym value: 0.036 / Net I/σ(I): 55.48 / Num. measured all: 291547 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.125 / Num. unique all: 3958 / Rsym value: 0.354 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F6F Resolution: 1.65→19.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.342 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.075 / 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: 24.478 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.654→1.697 Å / Total num. of bins used: 20
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