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Yorodumi- PDB-8qq1: SpNOX dehydrogenase domain, mutant F397W in complex with Flavin a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qq1 | ||||||||||||
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Title | SpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD) | ||||||||||||
Components | Oxidoreductase | ||||||||||||
Keywords | MEMBRANE PROTEIN / Streptococcus pneumoniae NADPH Oxidase (spNOX) Reactive oxygen species (ROS) membrane protein electron transfer oxidative stress | ||||||||||||
Function / homology | Function and homology information ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / membrane Similarity search - Function | ||||||||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å | ||||||||||||
Authors | Humm, A.S. / Dupeux, F. / Vermot, A. / Petit-Harleim, I. / Fieschi, F. / Marquez, J.A. | ||||||||||||
Funding support | France, European Union, 3items
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Citation | Journal: Elife / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qq1.cif.gz | 292.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qq1.ent.gz | 236.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qq1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8qq1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8qq1_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 8qq1_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/8qq1 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/8qq1 | HTTPS FTP |
-Related structure data
Related structure data | 8qq5C 8qq7C 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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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.) Streptococcus pneumoniae (bacteria) / Gene: ndoR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4J2B4U9 #2: Chemical | #3: Chemical | ChemComp-BR / #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: 2.54 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.941→36.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.142
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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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