[English] 日本語
Yorodumi- PDB-3dk9: Catalytic cycle of human glutathione reductase near 1 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dk9 | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic cycle of human glutathione reductase near 1 A resolution | ||||||
Components | Glutathione reductase | ||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / glutathione / nicotinamide / Alternative initiation / FAD / Flavoprotein / Mitochondrion / NADP / Phosphoprotein / Redox-active center / Transit peptide | ||||||
Function / homology | Function and homology information glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / NADP binding / flavin adenine dinucleotide binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.95 Å | ||||||
Authors | Berkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Catalytic cycle of human glutathione reductase near 1 A resolution. Authors: Berkholz, D.S. / Faber, H.R. / Savvides, S.N. / Karplus, P.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dk9.cif.gz | 244 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dk9.ent.gz | 193.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dk9_validation.pdf.gz | 713.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3dk9_full_validation.pdf.gz | 722 KB | Display | |
Data in XML | 3dk9_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3dk9_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk9 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk9 | HTTPS FTP |
-Related structure data
Related structure data | 3djgC 3djjC 3dk4C 3dk8C 3grsS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 51636.242 Da / Num. of mol.: 1 / Fragment: UNP residues 45 to 522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSR, GLUR, GRD1 / Production host: Escherichia coli (E. coli) References: UniProt: P00390, glutathione-disulfide reductase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 7 Details: 3% ammonium sulfate, 0.1 M potassium phosphate and 0.1% beta-octyl glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 290866 / % possible obs: 88 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 0.95→0.96 Å / Rmerge(I) obs: 0.347 / % possible all: 45.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 3GRS Resolution: 0.95→50 Å / Occupancy max: 1 / Occupancy min: 0.16 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.916 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→50 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|