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Yorodumi- PDB-3vln: Human Glutathione Transferase O1-1 C32S Mutant in Complex with As... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vln | ||||||
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Title | Human Glutathione Transferase O1-1 C32S Mutant in Complex with Ascorbic Acid | ||||||
Components | Glutathione S-transferase omega-1 | ||||||
Keywords | TRANSFERASE / GST fold / reductase / glutathione | ||||||
Function / homology | Function and homology information positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / Vitamin C (ascorbate) metabolism / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / glutathione metabolic process / oxidoreductase activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Brock, J. / Board, P.G. / Oakley, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases. Authors: Zhou, H. / Brock, J. / Liu, D. / Board, P.G. / Oakley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vln.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vln.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vln_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 3vln_full_validation.pdf.gz | 492.5 KB | Display | |
Data in XML | 3vln_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3vln_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/3vln ftp://data.pdbj.org/pub/pdb/validation_reports/vl/3vln | HTTPS FTP |
-Related structure data
Related structure data | 3q18C 3q19C 3qagC 1eemS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 27583.779 Da / Num. of mol.: 1 / Mutation: C32S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P78417, glutathione transferase |
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#3: Sugar | ChemComp-ASC / |
-Non-polymers , 5 types, 212 molecules
#2: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-ACT / | #7: 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: 2.38 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75 Details: 2.2M ammonium sulfate, 0.1M sodium acetate pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: BEAMLINE OPTICS |
Radiation | Monochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.29 Å / Num. all: 29768 / Num. obs: 29768 / % possible obs: 99.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.14 / Num. unique all: 2912 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EEM Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.773 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.695 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.7624 Å / Origin y: -10.6049 Å / Origin z: 19.8133 Å
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