+Open data
-Basic information
Entry | Database: PDB / ID: 1k4q | ||||||
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Title | Human Glutathione Reductase Inactivated by Peroxynitrite | ||||||
Components | Glutathione Reductase | ||||||
Keywords | OXIDOREDUCTASE / Nitrotyrosine / Flavoenzyme | ||||||
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 / cellular response to oxidative stress / flavin adenine dinucleotide binding / 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 / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Savvides, S.N. / Scheiwein, M. / Boehme, C.C. / Arteel, G.E. / Karplus, P.A. / Becker, K. / Schirmer, R.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the antioxidant enzyme glutathione reductase inactivated by peroxynitrite. Authors: Savvides, S.N. / Scheiwein, M. / Bohme, C.C. / Arteel, G.E. / Karplus, P.A. / Becker, K. / Schirmer, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k4q.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4q.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 1k4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4q ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4q | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the second pat of the biological assembly is generated by a crystallographic two-fold axis |
-Components
#1: Protein | Mass: 50068.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00390, EC: 1.6.4.2 |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.75 Å3/Da / Density % sol: 55.2 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium Sulfate, Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 41212 / Num. obs: 41212 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.2 / % possible all: 94.4 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 94.4 % / Rmerge(I) obs: 0.353 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: NIY 106 ALT CONF A and TYR 106 ALT CONF B exist as alternate conformations. Two conformations of NIY 114, ALT CONF A & B, AND TYR 114 ALT CONF C exist as alternate conformations.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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