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Yorodumi- PDB-2ab6: HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18) complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ab6 | ||||||
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Title | HUMAN GLUTATHIONE S-TRANSFERASE M2-2 (E.C.2.5.1.18) complexed with S-METHYLGLUTATHIONE | ||||||
Components | Glutathione S-transferase Mu 2 | ||||||
Keywords | TRANSFERASE / S-METHYLGLUTATHIONE / CONJUGATION / DETOXIFICATION | ||||||
Function / homology | Function and homology information nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione binding / hepoxilin biosynthetic process / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / 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 / negative regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase 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 / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Patskovsky, Y. / Almo, S.C. / Listowsky, I. | ||||||
Citation | Journal: To be Published Title: Structural Perturbations in the Active Site of Human Glutathione-S-Transferase M2-2 Upon Ligand Binding Authors: Patskovsky, Y. / Patskovska, L. / Almo, S.C. / Listowsky, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Expression, Crystallization and Preliminary X-Ray Analysis of Ligand-Free Human Glutathione S-Transferase M2-2 Authors: Patskovska, L.N. / Fedorov, A.A. / Patskovsky, Y.V. / Almo, S.C. / Listowsky, I. #2: 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. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ab6.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ab6.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ab6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/2ab6 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/2ab6 | HTTPS FTP |
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-Related structure data
Related structure data | 2gtuS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 217 / Label seq-ID: 1 - 217
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Details | The biological assembly is a homodimer composed of two identical monomers. The asymmetric unit contains two homodimers, composed of chains A/B and C/D, respectively. |
-Components
#1: Protein | Mass: 25645.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM2, GST4 / Plasmid: pET3a-GSTM2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28161, glutathione transferase #2: Chemical | ChemComp-GSM / #3: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 4000, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2004 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 28327 / Num. obs: 28327 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.13 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3927 / Rsym value: 0.41 / % possible all: 73.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GTU Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.814 / SU B: 14.608 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.388 / 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: 16.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1828 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
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