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Yorodumi- PDB-1m0u: Crystal Structure of the Drosophila Glutathione S-transferase-2 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m0u | ||||||
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Title | Crystal Structure of the Drosophila Glutathione S-transferase-2 in Complex with Glutathione | ||||||
Components | GST2 gene product | ||||||
Keywords | TRANSFERASE / GST / Flight Muscle Protein / Sigma | ||||||
Function / homology | Function and homology information Glutathione conjugation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-D synthase activity / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.75 Å | ||||||
Authors | Agianian, B. / Tucker, P.A. / Schouten, A. / Leonard, K. / Bullard, B. / Gros, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structure of a Drosophila Sigma Class Glutathione S-transferase Reveals a Novel Active Site Topography Suited for Lipid Peroxidation Products Authors: Agianian, B. / Tucker, P.A. / Schouten, A. / Leonard, K. / Bullard, B. / Gros, P. #1: Journal: Eur.J.Biochem. / Year: 2001 Title: Catalytic function of Drosophila melanogaster glutathione S-transferase DmGSTS1-1 (GST-2) in conjuction of lipid peroxidation end products Authors: Singh, S.P. / Coronella, J.A. / Benes, H. / Cochrane, B.J. / Zimniak, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m0u.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m0u.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/1m0u ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m0u | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains the biological dimer |
-Components
#1: Protein | Mass: 27640.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P41043, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-GSH / | #4: 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: 2.77 Å3/Da / Density % sol: 55.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, Sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Details: Agianian, B., (2001) Acta Crystallogr., D57, 725. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→76.7 Å / Num. all: 62202 / Num. obs: 62202 / % possible obs: 99.5 % / Rsym value: 0.039 |
Reflection shell | Resolution: 1.75→1.78 Å / Rsym value: 0.238 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 623131 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 9.14 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.75→70 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.202 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→70 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 70 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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