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Yorodumi- PDB-7wwy: M117L variant of Cu/Zn-superoxide dismutase from dog (Canis famil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wwy | ||||||
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Title | M117L variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | METAL BINDING PROTEIN / Superoxide dismutase / SOD / SOD1 / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / reactive oxygen species metabolic process / removal of superoxide radicals / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Narikiyo, S. / Furukawa, Y. / Akutsu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Intrinsic structural vulnerability in the hydrophobic core induces species-specific aggregation of canine SOD1 with degenerative myelopathy-linked E40K mutation. Authors: Hashimoto, K. / Watanabe, S. / Akutsu, M. / Muraki, N. / Kamishina, H. / Furukawa, Y. / Yamanaka, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wwy.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wwy.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/7wwy ftp://data.pdbj.org/pub/pdb/validation_reports/ww/7wwy | HTTPS FTP |
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-Related structure data
Related structure data | 7wwtC 7wx0C 7wx1C 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
#1: Protein | Mass: 15846.670 Da / Num. of mol.: 2 / Mutation: M117L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SOD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WNN6, superoxide dismutase #2: Chemical | #3: Chemical | #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: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Sodium malonate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.275 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.275 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.85 Å / Num. obs: 60359 / % possible obs: 99.5 % / Redundancy: 32.3 % / CC1/2: 1 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.5→1.58 Å / Num. unique obs: 8347 / CC1/2: 0.533 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→47.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.712 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / 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: 29.788 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→47.71 Å
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