+Open data
-Basic information
Entry | Database: PDB / ID: 2qx9 | ||||||
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Title | Crystal Structure of Quinone Reductase II | ||||||
Components | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||
Keywords | OXIDOREDUCTASE / Cytoplasm / FAD / Flavoprotein / Metal-binding / Polymorphism / Zinc | ||||||
Function / homology | Function and homology information ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å | ||||||
Authors | Calamini, B. / Santarsiero, B.D. / Boutin, J.A. / Mesecar, A.D. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2. Authors: Calamini, B. / Santarsiero, B.D. / Boutin, J.A. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qx9.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qx9.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qx9 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qx9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is a dimer of chains A and B in the asymmetric unit |
-Components
#1: Protein | Mass: 25849.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16083, EC: 1.10.99.2 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: BisTris, NaCl, Ammonium sulfate, 2-iodomelatonin, DTT, FAD, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→20 Å / Num. obs: 22987 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 33.286 Å2 / Rmerge(I) obs: 0.203 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.19→2.32 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 18751 / Num. unique obs: 3619 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Resolution: 2.31→20 Å / FOM work R set: 0.767 / σ(F): 0
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Solvent computation | Bsol: 65.987 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.829 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→20 Å
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Refine LS restraints |
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Xplor file |
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