+Open data
-Basic information
Entry | Database: PDB / ID: 4zvn | ||||||
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Title | Reduced quinone reductase 2 in complex with acridine orange | ||||||
Components | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||
Keywords | Oxidoreductase/oxidoreductase Inhibitor / quinone reductase 2 / acridine orange / Oxidoreductase-Inhibitor complex / Oxidoreductase-oxidoreductase Inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.866 Å | ||||||
Model details | Metallo-flavoprotein | ||||||
Authors | Leung, K.K. / Shilton, B.H. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2. Authors: Leung, K.K. / Shilton, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zvn.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvn.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 4zvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvn ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvn | HTTPS FTP |
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-Related structure data
Related structure data | 4zvkC 4zvlC 4zvmC 1qr2S 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
#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: pProEXhta / 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 / | Sequence details | The mismatch between F46 (in the deposited structure) and L47 (from UNP P16083) is due to SNP ...The mismatch between F46 (in the deposited structure) and L47 (from UNP P16083) is due to SNP rs1143684. Both forms of NQO2 are found in the population where F46 is the predominant form in the population. For your reference-1. Megarity, C. F., Gill, J. R. E., Caraher, M. C., Stratford, I. J., Nolan, K. a, and Timson, D. J. (2014) The two common polymorphic forms of human NRH-quinone oxidoreductase 2 (NQO2) have different biochemical properties. FEBS Lett. 588, 1666 | |
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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: 2.41 Å3/Da / Density % sol: 48.98 % / Description: Yellow rods. Turns clear upon reduction |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.7M Ammonium sulfate, 0.1M Hepes |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å | |||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Osmic Confocol Max-Flux (CMF) graphite monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.86→19.51 Å / Num. obs: 42288 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Net I/σ(I): 15.9 / Num. measured all: 288908 / Scaling rejects: 222 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QR2 Resolution: 1.866→19.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.38 Å2 / Biso mean: 21.1895 Å2 / Biso min: 6.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.866→19.51 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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