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- PDB-8cap: Crystal structure of dehydrogenase domain of Cylindrospermum stag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cap | |||||||||
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Title | Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with CB28 | |||||||||
![]() | Putative ferric reductase | |||||||||
![]() | OXIDOREDUCTASE / ROS / inhibitor / redox biology | |||||||||
Function / homology | ![]() superoxide-generating NAD(P)H oxidase activity / NADPH oxidase complex / superoxide anion generation / defense response / nucleotide binding / calcium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Reis, J. / Mattevi, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting ROS production through inhibition of NADPH oxidases. Authors: Reis, J. / Gorgulla, C. / Massari, M. / Marchese, S. / Valente, S. / Noce, B. / Basile, L. / Torner, R. / Cox 3rd, H. / Viennet, T. / Yang, M.H. / Ronan, M.M. / Rees, M.G. / Roth, J.A. / ...Authors: Reis, J. / Gorgulla, C. / Massari, M. / Marchese, S. / Valente, S. / Noce, B. / Basile, L. / Torner, R. / Cox 3rd, H. / Viennet, T. / Yang, M.H. / Ronan, M.M. / Rees, M.G. / Roth, J.A. / Capasso, L. / Nebbioso, A. / Altucci, L. / Mai, A. / Arthanari, H. / Mattevi, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.8 KB | Display | ![]() |
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PDB format | ![]() | 171.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cakC ![]() 8calC ![]() 8caoC ![]() 8cb0C 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 32230.916 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-U4O / [ Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: Hepes 0.1 mM pH 7.5, 0.3 M sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate, 20% (v/v) glycerol, 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 1, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3→49.024 Å / Num. obs: 24161 / % possible obs: 96.4 % / Redundancy: 4.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.124 / Rrim(I) all: 0.284 / Net I/σ(I): 5.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 143.82 Å2 / Biso mean: 72.1108 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.024 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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