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Yorodumi- PDB-8c9j: Crystal structure of human NQO1 by serial femtosecond crystallography -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c9j | |||||||||
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Title | Crystal structure of human NQO1 by serial femtosecond crystallography | |||||||||
Components | NAD(P)H dehydrogenase [quinone] 1 | |||||||||
Keywords | OXIDOREDUCTASE / NQO1 / flavoprotein / cancer / serial femtosecond crystallography / microcrystals / XFEL / Droplet injection | |||||||||
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 / xenobiotic metabolic process / removal of superoxide radicals / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Martin-Garcia, J.M. / Grieco, A. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Pey, A. / Botha, S. / Ros, A. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Lab Chip / Year: 2023 Title: Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / ...Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / Nelson, G. / Yang, J.H. / Carrion, J. / Morin, K. / Ketawala, G.K. / Pey, A.L. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Hermoso, J.A. / Nazari, R. / Sierra, R. / Hunter, M.S. / Batyuk, A. / Kupitz, C.J. / Sublett, R.E. / Lisova, S. / Mariani, V. / Boutet, S. / Fromme, R. / Grant, T.D. / Botha, S. / Fromme, P. / Kirian, R.A. / Martin-Garcia, J.M. / Ros, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c9j.cif.gz | 242 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c9j.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 8c9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/8c9j ftp://data.pdbj.org/pub/pdb/validation_reports/c9/8c9j | HTTPS FTP |
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-Related structure data
Related structure data | 8fwaC 1dxqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 30907.611 Da / Num. of mol.: 4 / Mutation: None Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO1, DIA4, NMOR1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.65 Å3/Da / Density % sol: 53.52 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350, 20 um FAD |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.2848 Å |
Detector | Type: SLAC ePix10k / Detector: PIXEL / Date: May 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2848 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→24 Å / Num. obs: 36928 / % possible obs: 100 % / Redundancy: 46 % / CC1/2: 0.9668 / CC star: 0.9234 / Net I/σ(I): 1.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 3619 / CC1/2: 0.458 / CC star: 0.5202 / % possible all: 100 |
Serial crystallography sample delivery | Description: Modular Droplet Injector / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Crystals in mother liquor encapsulated into oil droplets Crystal conc.: 1000 / Description: Modular Droplet Injector / Flow rate: 5 µL/min / Injector temperature: 298 K |
Serial crystallography data reduction | XFEL pulse events: 40 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DXQ Resolution: 2.7→23.922 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.878 / SU B: 28.385 / SU ML: 0.508 / Cross valid method: FREE R-VALUE / ESU R Free: 0.377 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→23.922 Å
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Refine LS restraints |
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Refine LS restraints NCS | Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Weight Biso : 0.866 / Weight position: 0.0866
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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