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Yorodumi- PDB-7dw1: Crystal structure of a glutathione S-transferase SbGSTU6 from Sal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dw1 | ||||||
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Title | Crystal structure of a glutathione S-transferase SbGSTU6 from Salix babylonica in complex with glutathione | ||||||
Components | Glutathione S-transferase | ||||||
Keywords | TRANSFERASE / Enzyme | ||||||
Function / homology | Function and homology information response to chemical / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Salix babylonica (weeping willow) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Zhuge, X.L. / Yang, H.L. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of a glutathione S-transferase SbGSTU6 from Salix babylonica in complex with glutathione Authors: Zhuge, X.L. / Yang, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dw1.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dw1.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/7dw1 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/7dw1 | HTTPS FTP |
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-Related structure data
Related structure data | 7dw3C 5kejS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26354.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salix babylonica (weeping willow) / Gene: GSTU6 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y5R032 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: L-Proline, magnesium, HEFHS, sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30.9 Å / Num. obs: 17442 / % possible obs: 82.1 % / Redundancy: 6.56 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 1 / Net I/σ(I): 1.46 |
Reflection shell | Resolution: 2.27→2.59 Å / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KEJ Resolution: 2.27→30.9 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.7374 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 45.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→30.9 Å
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Refine LS restraints |
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LS refinement shell |
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