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Yorodumi- PDB-3gur: Crystal Structure of mu class glutathione S-transferase (GSTM2-2)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gur | ||||||
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Title | Crystal Structure of mu class glutathione S-transferase (GSTM2-2) in complex with glutathione and 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX) | ||||||
Components | Glutathione S-transferase Mu 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / GSTM2-2-inhibitor complex / glutathione-NBDHEX covalent complex (sigma-complex) / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / 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 / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Federici, L. / Lo Sterzo, C. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M. | ||||||
Citation | Journal: Cancer Res. / Year: 2009 Title: Structural basis for the binding of the anticancer compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol to human glutathione s-transferases Authors: Federici, L. / Lo Sterzo, C. / Pezzola, S. / Di Matteo, A. / Scaloni, F. / Federici, G. / Caccuri, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gur.cif.gz | 189.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gur.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3gur ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3gur | HTTPS FTP |
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-Related structure data
Related structure data | 3gusC 3ie3C 1hncS C: citing same article (ref.) 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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-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) / Plasmid: pGST-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28161, glutathione transferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16% PEG 8000, 200mM NaCl, 100mM MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→109.7 Å / Num. all: 32108 / Num. obs: 32108 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.32 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.01 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNC Resolution: 2.5→29.43 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.877 / SU B: 9.875 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 2.07 / ESU R Free: 0.354 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.211 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.504→2.569 Å / Total num. of bins used: 20
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