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Open data
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Basic information
Entry | Database: PDB / ID: 8rfm | |||||||||
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Title | Human NOQ1 enzyme in complex with NADH by serial crystallography | |||||||||
![]() | NAD(P)H dehydrogenase [quinone] 1 | |||||||||
![]() | FLAVOPROTEIN / NQO1 / oxidoreductase / redox mechanism / flavoenzyme | |||||||||
Function / homology | ![]() 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) / negative regulation of ferroptosis / 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 / response to hormone / 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 / neuronal cell body / synapse / dendrite / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Martin-Garcia, J.M. / Grieco, A. / Medina, M. / Boneta, S. / Pey, A.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations. Authors: Grieco, A. / Boneta, S. / Gavira, J.A. / Pey, A.L. / Basu, S. / Orlans, J. / Sanctis, D. / Medina, M. / Martin-Garcia, J.M. #1: ![]() Title: Human NOQ1 enzyme in complex with NADH by serial crystallography Authors: Martin-Garcia, J.M. / Grieco, A. / Medina, M. / Boneta, S. / Pey, A.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.8 KB | Display | ![]() |
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PDB format | ![]() | 187.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8rfnC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30907.611 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P15559, NAD(P)H dehydrogenase (quinone) #2: Chemical | ChemComp-FAD / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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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 |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 18, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→98 Å / Num. obs: 32476 / % possible obs: 100 % / Redundancy: 154.1 % / Biso Wilson estimate: 75.6 Å2 / CC star: 0.977 / R split: 0.154 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.7→2.77 Å / Num. unique obs: 32476 / CC star: 0.523 / R split: 0.976 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: small SOS chips |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.395 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→98 Å
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