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Yorodumi- PDB-7b4o: A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b4o | |||||||||
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Title | A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn metalation | |||||||||
Components | Superoxide dismutase [Cu-Zn] | |||||||||
Keywords | OXIDOREDUCTASE / Superoxide dismutase / copper / zinc / bacterial | |||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacteroidetes bacterium GWA2_30_7 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | |||||||||
Authors | Wright, G.S.A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol.Biol.Evol. / Year: 2021 Title: Bacterial Evolutionary Precursors of Eukaryotic Copper-Zinc Superoxide Dismutases. Authors: Wright, G.S.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b4o.cif.gz | 433.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b4o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/7b4o ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b4o | HTTPS FTP |
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-Related structure data
Related structure data | 7b4pC 2c9vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 4 - 153 / Label seq-ID: 4 - 153
NCS ensembles :
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-Components
#1: Protein | Mass: 16240.186 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroidetes bacterium GWA2_30_7 (bacteria) Gene: A2046_17220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1F3DVA5, superoxide dismutase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM tris(hydroxymethyl)aminomethane-HCl, 20 % polyethylene glycol 6000, 2 mM ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→68.27 Å / Num. obs: 122059 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 5982 / CC1/2: 0.345 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2c9v Resolution: 1.41→68.27 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.347 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.058 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.872 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→68.27 Å
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Refine LS restraints |
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