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Yorodumi- PDB-4mpg: Crystal structure of human glutathione transferase theta-2, compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mpg | ||||||
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Title | Crystal structure of human glutathione transferase theta-2, complex with glutathione and unknown ligand, target EFI-507257 | ||||||
Components | Glutathione S-transferase theta-2 | ||||||
Keywords | TRANSFERASE / Glutathione S-transferase / Enzyme Function Initiative / EFI / structural genomics | ||||||
Function / homology | Function and homology information Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Glutathione S-Transferase Theta-2 (Target EFI-507257) Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mpg.cif.gz | 223.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mpg.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/4mpg ftp://data.pdbj.org/pub/pdb/validation_reports/mp/4mpg | HTTPS FTP |
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-Related structure data
Related structure data | 1ljrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 30112.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0CG29, UniProt: P0CG30*PLUS, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-FMT / | #5: 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: 2.51 Å3/Da / Density % sol: 51.08 % |
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Crystal grow | pH: 7 Details: Protein in 10 mM HEPES, pH 7.5, 150 MM sodium chloride, 5% glycerol, reservoir: 2M sodium formate, 0.1M BIS-TRIS propane:HCl, pH 7.0, 5 mM GSH, cryoprotectant: none, vapor diffusion, sitting ...Details: Protein in 10 mM HEPES, pH 7.5, 150 MM sodium chloride, 5% glycerol, reservoir: 2M sodium formate, 0.1M BIS-TRIS propane:HCl, pH 7.0, 5 mM GSH, cryoprotectant: none, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2013 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 44270 / % possible obs: 99.7 % / Observed criterion σ(I): -5 / Redundancy: 12.1 % / Rsym value: 0.056 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LJR Resolution: 1.951→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.39 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / 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: 61.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.951→50 Å
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