[English] 日本語
Yorodumi- PDB-3gtu: LIGAND-FREE HETERODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M2-3 (E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gtu | ||||||
---|---|---|---|---|---|---|---|
Title | LIGAND-FREE HETERODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M2-3 (EC 2.5.1.18), MONOCLINIC CRYSTAL FORM | ||||||
Components | (GLUTATHIONE S-TRANSFERASE) x 2 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / HETERODIMER | ||||||
Function / homology | Function and homology information establishment of blood-nerve barrier / sperm fibrous sheath / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione derivative biosynthetic process / glutathione binding / hepoxilin biosynthetic process / linoleic acid metabolic process / Glutathione conjugation ...establishment of blood-nerve barrier / sperm fibrous sheath / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione derivative biosynthetic process / glutathione binding / hepoxilin biosynthetic process / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge / positive regulation of ryanodine-sensitive calcium-release channel activity / cellular response to caffeine / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / response to estrogen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: An asparagine-phenylalanine substitution accounts for catalytic differences between hGSTM3-3 and other human class mu glutathione S-transferases. Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal Structure of Human Class Mu Glutathione Transferase Gstm2-2. Effects of Lattice Packing on Conformational Heterogeneity Authors: Raghunathan, S. / Chandross, R.J. / Kretsinger, R.H. / Allison, T.J. / Penington, C.J. / Rule, G.S. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Cloning, Expression, and Characterization of a Class-Mu Glutathione Transferase from Human Muscle, the Product of the Gst4 Locus Authors: Vorachek, W.R. / Pearson, W.R. / Rule, G.S. #3: Journal: J.Biol.Chem. / Year: 1990 Title: A Distinct Human Testis and Brain Mu-Class Glutathione S-Transferase. Molecular Cloning and Characterization of a Form Present Even in Individuals Lacking Hepatic Type Mu Isoenzymes Authors: Campbell, E. / Takahashi, Y. / Abramovitz, M. / Peretz, M. / Listowsky, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gtu.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gtu.ent.gz | 151.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gtu_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gtu_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 3gtu_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 3gtu_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gtu ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gtu | HTTPS FTP |
-Related structure data
Related structure data | 4gtuC 2gtuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 25645.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LIGAND-FREE, HETERODIMER / Source: (gene. exp.) Homo sapiens (human) Description: THE GSTM2 AND GSTM3 CDNA WERE AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A COEXPRESSION VECTOR. SYNTHETIC GENE. Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM2, GSTM3 / Plasmid: PET3A-GSTM2-3 / Species (production host): Escherichia coli / Gene (production host): GSTM2, GSTM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28161, glutathione transferase #2: Protein | Mass: 26460.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LIGAND-FREE, HETERODIMER / Source: (gene. exp.) Homo sapiens (human) Description: THE GSTM2 AND GSTM3 CDNA WERE AMPLIFIED USING RT-PCR AND SUBCLONED INTO A PET3A COEXPRESSION VECTOR. SYNTHETIC GENE. Cell line: HELA / Cellular location: CYTOPLASM / Gene: GSTM2, GSTM3 / Plasmid: PET3A-GSTM2-3 / Species (production host): Escherichia coli / Gene (production host): GSTM2, GSTM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P21266, glutathione transferase #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 289 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jul 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→10 Å / Num. obs: 25387 / % possible obs: 94.41 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.71 % / Rmerge(I) obs: 0.341 / % possible all: 69.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GTU Resolution: 2.8→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|