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Yorodumi- PDB-8cak: Crystal structure of dehydrogenase domain of Cylindrospermum stag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cak | |||||||||
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Title | Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M41 | |||||||||
Components | Putative ferric reductase | |||||||||
Keywords | OXIDOREDUCTASE / ROS / inhibitor / redox biology | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cylindrospermum stagnale BEA 0605B (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 | 8cak.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cak.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 8cak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/8cak ftp://data.pdbj.org/pub/pdb/validation_reports/ca/8cak | HTTPS FTP |
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-Related structure data
Related structure data | 8calC 8caoC 8capC 8cb0C 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
-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 BEA 0605B (bacteria) Gene: Cylst_1289 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K9WT99 |
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-Non-polymers , 5 types, 28 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-U4F / | ||||
#4: Chemical | #5: Chemical | ChemComp-DMS / | #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 | Density Matthews: 5.1 Å3/Da / Density % sol: 75.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1.000002 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 1, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.000002 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.67→47.76 Å / Num. obs: 19417 / % possible obs: 99.6 % / Redundancy: 11.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.061 / Rrim(I) all: 0.207 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→47.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.052 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 135.3 Å2 / Biso mean: 53.632 Å2 / Biso min: 23.08 Å2
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Refinement step | Cycle: final / Resolution: 2.67→47.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.738 Å / Rfactor Rfree error: 0
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