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Yorodumi- PDB-3dk4: Catalytic cycle of human glutathione reductase near 1 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dk4 | ||||||
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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: 1.2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dk4.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dk4.ent.gz | 205.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dk4_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3dk4_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 3dk4_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 3dk4_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk4 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk4 | HTTPS FTP |
-Related structure data
Related structure data | 3djgC 3djjC 3dk8C 3dk9SC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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 |
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-Non-polymers , 5 types, 897 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-FAD / | ||
#4: Chemical | ChemComp-NDP / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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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 |
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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: 1.1→50 Å / Num. obs: 192443 / % possible obs: 91 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.1→1.12 Å / Rmerge(I) obs: 0.33 / % possible all: 74.8 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3DK9 Resolution: 1.2→50 Å / Occupancy max: 1 / Occupancy min: 0.11 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.332 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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