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Yorodumi- PDB-1dxo: Crystal structure of human NAD[P]H-QUINONE oxidoreductase CO with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dxo | ||||||
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Title | Crystal structure of human NAD[P]H-QUINONE oxidoreductase CO with 2,3,5,6,tetramethyl-P-benzoquinone (duroquinone) at 2.5 Angstrom resolution | ||||||
Components | QUINONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / cellular response to metal ion / NADH oxidation / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / synaptic transmission, cholinergic / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / removal of superoxide radicals / xenobiotic metabolic process / response to nutrient / cell redox homeostasis / response to hormone / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å | ||||||
Authors | Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S. / Ross, D. / Amzel, L.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structures of Recombinant Mouse and Human Nad(P)H:Quinone Oxidoreductases:Species Comparison and Structural Changes with Substrate Binding and Release Authors: Faig, M. / Bianchet, M.A. / Chen, S. / Winski, S. / Ross, D. / Talalay, P. / Amzel, L.M. #1: Journal: Biochem.Soc.Trans. / Year: 1999 Title: Structure and Mechanism of Cytosolic Quinone Reductase Authors: Bianchet, M.A. / Foster, C. / Faig, M. / Talalay, P. / Amzel, L.M. #2: Journal: Biochemistry / Year: 1999 Title: Crystal Structure of Human Quinone Reductase Type 2, a Metalloprotein Authors: Foster, C. / Bianchet, M.A. / Talalay, P. / Zhao, Q. / Amzel, L.M. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: The Three-Dimensional Structure of Nad(P)H:Quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction Authors: Li, R. / Bianchet, M.A. / Talalay, P. / Amzel, L.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET IN CHAIN A SHEETS B AND B1 REPRESENT ONE BIFURCATED SHEET IN CHAIN D SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET IN CHAIN C SHEETS D AND D1 REPRESENT ONE BIFURCATED SHEET IN CHAIN D |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxo.cif.gz | 225.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxo.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxo_validation.pdf.gz | 710.3 KB | Display | wwPDB validaton report |
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Full document | 1dxo_full_validation.pdf.gz | 750.8 KB | Display | |
Data in XML | 1dxo_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 1dxo_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxo ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxo | HTTPS FTP |
-Related 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: 30776.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15559, EC: 1.6.99.2 #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-DQN / #4: 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: 48.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.66 Å / Num. obs: 36969 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.093 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.5→27.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 411877.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19 Å2 / ksol: 0.30878 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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