[English] 日本語
Yorodumi- PDB-2c3q: Human glutathione-S-transferase T1-1 W234R mutant, complex with S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c3q | ||||||
---|---|---|---|---|---|---|---|
Title | Human glutathione-S-transferase T1-1 W234R mutant, complex with S- hexylglutathione | ||||||
Components | GLUTATHIONE S-TRANSFERASE THETA 1 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / GLUTATHIONE TRANSFERASE / T1-1 / POLYMORPHISM | ||||||
Function / homology | Function and homology information Glutathione conjugation / Paracetamol ADME / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Tars, K. / Larsson, A.-K. / Shokeer, A. / Olin, B. / Mannervik, B. / Kleywegt, G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis of the Suppressed Catalytic Activity of Wild-Type Human Glutathione Transferase T1-1 Compared to its W234R Mutant. Authors: Tars, K. / Larsson, A.-K. / Shokeer, A. / Olin, B. / Mannervik, B. / Kleywegt, G.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c3q.cif.gz | 209.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c3q.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 2c3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/2c3q ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c3q | HTTPS FTP |
---|
-Related structure data
Related structure data | 2c3nSC 2c3tC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 28300.068 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P30711, glutathione transferase #2: Chemical | ChemComp-GTX / #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TRP 233 TO ARG ENGINEERED RESIDUE IN CHAIN B, TRP 233 TO ARG ...ENGINEERED | Has ligand of interest | Y | Sequence details | 6XHIS TAG ADDED TO THE N-TERMINUS OF PROTEIN. RESIDUE TRP 234 MUTATED TO ARGININE. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.19 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE, 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350, 200 MM MG(NO3)2, 200 MM NAI AND 2 MM DITHIOTHREITOL] WERE MIXED WITH 5 MICROLITRES OF PROTEIN ...Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE, 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350, 200 MM MG(NO3)2, 200 MM NAI AND 2 MM DITHIOTHREITOL] WERE MIXED WITH 5 MICROLITRES OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8, 15 % GLYCEROL), 1 MICROLITRE 100 MM CACL2 AND 1 MICROLITRE 20 MM S-HEXYLGLUTATHIONE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.94 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 82135 / % possible obs: 90.5 % / Observed criterion σ(I): 2.3 / Redundancy: 1.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 82.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C3N Resolution: 1.85→28.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.283 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→28.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|