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- PDB-8qq1: SpNOX dehydrogenase domain, mutant F397W in complex with Flavin a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qq1 | ||||||||||||
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Title | SpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD) | ||||||||||||
![]() | Oxidoreductase | ||||||||||||
![]() | MEMBRANE PROTEIN / Streptococcus pneumoniae NADPH Oxidase (spNOX) Reactive oxygen species (ROS) membrane protein electron transfer oxidative stress | ||||||||||||
Function / homology | ![]() ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Humm, A.S. / Dupeux, F. / Vermot, A. / Petit-Harleim, I. / Fieschi, F. / Marquez, J.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX. Authors: Petit-Hartlein, I. / Vermot, A. / Thepaut, M. / Humm, A.S. / Dupeux, F. / Dupuy, J. / Chaptal, V. / Marquez, J.A. / Smith, S.M.E. / Fieschi, F. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.7 KB | Display | ![]() |
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PDB format | ![]() | 236.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 45.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qq5C ![]() 8qq7C 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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Unit cell |
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Components
#1: Protein | Mass: 25643.154 Da / Num. of mol.: 3 / Mutation: F397W Source method: isolated from a genetically manipulated source Details: Flavin Adenin dinucleotide / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-BR / #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: 2.54 Å3/Da / Density % sol: 51.5 % Description: typical crystal shape are elongated hexagon, 150 micrometr lenght 80 micrometer wide. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystals Obtained at the HTX Facility, EMBL Grenoble 17% w/v PEG3350, 0.1M BIS-TRIS Propane pH6.5, 0.2M Sodium bromide. Automatic harvesting and cryocooling with CrystalDirect |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2018 / Details: Vertical CRL / Horizontal elliptical mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.941→58.944 Å / Num. obs: 57719 / % possible obs: 98.4 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.023 / Rrim(I) all: 0.119 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.941→1.974 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.829 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2772 / CC1/2: 0.723 / Rpim(I) all: 0.372 / % possible all: 95.6 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 38.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.941→36.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.941→1.96 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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