[English] 日本語
Yorodumi- PDB-1u3i: Crystal structure of glutathione S-tranferase from Schistosoma mansoni -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u3i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of glutathione S-tranferase from Schistosoma mansoni | ||||||
Components | Glutathione S-transferase 28 kDa | ||||||
Keywords | TRANSFERASE / GST fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Chomilier, J. / Vaney, M.C. / Labesse, G. / Trottein, F. / Capron, A. / Mormon, J.-P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Schistosoma mansoni glutathione S-transferase Authors: Chomilier, J. / Vaney, M.C. / Labesse, G. / Trottein, F. / Capron, A. / Mormon, J.-P. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization and preliminary X-ray diffraction studies of a protective cloned 28 kDa glutathione S-transferase from Schistosoma mansoni Authors: Trottein, F.M. / Vaney, M.C. / Bachet, B. / Pierce, R.-J. / Colloc'h, N. / Lecocq, J.-P. / Capron, A. / Mormon, J.-P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1u3i.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1u3i.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1u3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/1u3i ftp://data.pdbj.org/pub/pdb/validation_reports/u3/1u3i | HTTPS FTP |
---|
-Related structure data
Related structure data | 1oe8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | The second part of the biological assembly is generated by the two fold axis: z-1/4,3/4-y,1/4+x |
-Components
#1: Protein | Mass: 23893.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pTG54 / Production host: Escherichia coli (E. coli) / Strain (production host): TGE901 / References: UniProt: P09792, glutathione transferase |
---|---|
#2: Chemical | ChemComp-GSH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: ammonium sulfate, potassium phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1992 |
Radiation | Monochromator: Curved Si (111) - multilayers mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→19.78 Å / Num. all: 24391 / Num. obs: 24391 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.067 |
Reflection shell | Resolution: 1.89→1.97 Å / Num. unique all: 2483 / Rsym value: 0.407 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE8 Resolution: 1.89→19.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.147 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.106 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2517 Å / Luzzati d res low obs: 1.89 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→19.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|