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Yorodumi- PDB-8imd: Crystal structure of Cu/Zn Superoxide dismutase from Paenibacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8imd | ||||||
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Title | Crystal structure of Cu/Zn Superoxide dismutase from Paenibacillus lautus | ||||||
Components | Cu/Zn-Superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / Superoxide dismutase / SOD / SOD1 | ||||||
Function / homology | COPPER (II) ION Function and homology information | ||||||
Biological species | Paenibacillus lautus NBRC 15380 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Narikiyo, S. / Furukawa, Y. / Akutsu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Characterization of a novel cysteine-less Cu/Zn-superoxide dismutase in Paenibacillus lautus missing a conserved disulfide bond. Authors: Furukawa, Y. / Shintani, A. / Narikiyo, S. / Sue, K. / Akutsu, M. / Muraki, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8imd.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8imd.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 8imd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8imd_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8imd_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8imd_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 8imd_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/8imd ftp://data.pdbj.org/pub/pdb/validation_reports/im/8imd | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23267.592 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus lautus NBRC 15380 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.21 Å3/Da / Density % sol: 44.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 22.5% PEG 4,000, 100 mM acetic acid and sodium acetate buffer |
-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 23, 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: 1.45→45.31 Å / Num. obs: 74112 / % possible obs: 99.8 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 15.9 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10562 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→45.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.493 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / 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: 23.781 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→45.35 Å
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Refine LS restraints |
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