+Open data
-Basic information
Entry | Database: PDB / ID: 1dxq | ||||||
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Title | CRYSTAL STRUCTURE OF MOUSE NAD[P]H-QUINONE OXIDOREDUCTASE | ||||||
Components | QUINONE REDUCTASE | ||||||
Keywords | FLAVOPROTEIN / DT-DIAPHORASE / CANCER / CHEMOPROTECTION / CHEMOTHERAPY / DEHYDROGENASEROSSMAN FOLD / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Regulation of ornithine decarboxylase (ODC) / response to L-glutamine / response to flavonoid / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / NADPH oxidation / : / response to tetrachloromethane ...Regulation of ornithine decarboxylase (ODC) / response to L-glutamine / response to flavonoid / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / NADPH oxidation / : / response to tetrachloromethane / response to xenobiotic stimulus => GO:0009410 / NADH:ubiquinone reductase (non-electrogenic) activity / negative regulation of catalytic activity / NAD(P)H dehydrogenase (quinone) activity / response to hydrogen sulfide / response to alkaloid / response to carbohydrate / superoxide metabolic process / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / response to nutrient / cell redox homeostasis / response to hormone / response to ischemia / cellular response to hydrogen peroxide / positive regulation of neuron apoptotic process / response to estradiol / response to ethanol / response to oxidative stress / response to xenobiotic stimulus / neuronal cell body / dendrite / negative regulation of apoptotic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 1dxq.cif.gz | 225.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxq.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxq ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxq | HTTPS FTP |
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-Related structure data
Related structure data | 1d4aC 1dxoC 1qrdS 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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2 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: DIMERIC |
-Components
#1: Protein | Mass: 30850.408 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q64669, EC: 1.6.99.2 #2: Chemical | ChemComp-FAD / |
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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: 48.19 % | ||||||||||||||||||||||||||||||||||||||||
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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 RUH2R / Wavelength: 1.5418 |
Detector | Type: R-AXIS IV / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.98 Å / Num. obs: 18847 / % possible obs: 66.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.1 |
Reflection | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QRD Resolution: 2.8→42.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1633136.18 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.290322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→42.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.055 / 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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