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Yorodumi- PDB-4cf6: Crystal structure of the complex of the P187S variant of human NA... -
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-Basic information
Entry | Database: PDB / ID: 4cf6 | ||||||
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Title | Crystal structure of the complex of the P187S variant of human NAD(P) H:quinone oxidoreductase with Cibacron blue at 2.7 A resolution | ||||||
Components | NAD(P)H DEHYDROGENASE [QUINONE] 1 | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / SINGLE AMINO ACID EXCHANGE | ||||||
Function / homology | Function and homology information response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / 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 / synaptic transmission, cholinergic / response to alkaloid / response to carbohydrate / 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 / xenobiotic metabolic process / removal of superoxide radicals / response to hormone / response to nutrient / cell redox homeostasis / 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 / dendrite / neuronal cell body / synapse / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.694 Å | ||||||
Authors | Lienhart, W.D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P. | ||||||
Citation | Journal: FEBS J. / Year: 2014 Title: Collapse of the Native Structure by a Single Amino Acid Exchange in Human Nad(P)H:Quinone Oxidoreductase (Nqo1). Authors: Lienhart, W.D. / Gudipati, V. / Uhl, M.K. / Binter, A. / Pulido, S. / Saf, R. / Zangger, K. / Gruber, K. / Macheroux, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cf6.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cf6.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/4cf6 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/4cf6 | HTTPS FTP |
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-Related structure data
Related structure data | 4cetSC S: Starting model for refinement C: citing same article (ref.) |
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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: 33068.934 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) #2: Chemical | #3: Chemical | #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: 2.4 Å3/Da / Density % sol: 48.79 % / Description: NONE |
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Crystal grow | pH: 7 / Details: PROTEIN WAS CRYSTALLIZED FROM 60% TACSIMATE PH=7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection twin | Operator: -K,-H,-L / Fraction: 0.39 |
Reflection | Resolution: 2.69→26.74 Å / Num. obs: 18149 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.69→2.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.4 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CET Resolution: 2.694→46.217 Å / σ(F): 1.34 / Phase error: 32.54 / Stereochemistry target values: TWIN_LSQ_F
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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 mean: 42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.694→46.217 Å
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Refine LS restraints |
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LS refinement shell |
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