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Yorodumi- PDB-8cb0: Crystal structure of dehydrogenase domain of Cylindrospermum stag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cb0 | |||||||||
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Title | Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M41 and NADP+ | |||||||||
Components | Putative ferric reductase | |||||||||
Keywords | OXIDOREDUCTASE / ROS / inhibitor / redox biology | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cylindrospermum stagnale (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Reis, J. / Mattevi, A. | |||||||||
Funding support | Italy, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cb0.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cb0.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 8cb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/8cb0 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/8cb0 | HTTPS FTP |
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-Related structure data
Related structure data | 8cakSC 8calC 8caoC 8capC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32230.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cylindrospermum stagnale (bacteria) / Gene: Cylst_1289 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K9WT99 |
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-Non-polymers , 5 types, 52 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-U4F / | ||||
#4: Chemical | #5: Chemical | ChemComp-NAP / | #6: Water | ChemComp-HOH / | |
-Details
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 grow | Temperature: 293 K / Method: evaporation / pH: 8 Details: 0.3 M diethylene glycol; 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, Tris-HCl 0.1 M pH 8.0, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.21 Å / Num. obs: 24102 / % possible obs: 99.9 % / Redundancy: 20.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.039 / Rrim(I) all: 0.177 / Χ2: 0.97 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible obs: 100 % / Redundancy: 21.3 % / Rmerge(I) obs: 2.676 / Num. measured all: 57425 / Num. unique obs: 2693 / CC1/2: 0.526 / Rpim(I) all: 0.592 / Rrim(I) all: 2.742 / Χ2: 0.94 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8CAK Resolution: 2.5→72.21 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.262 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 51.514 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→72.21 Å
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Refine LS restraints |
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