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Yorodumi- PDB-8avn: Mutant of Superoxide dismutase SodFM1 from CPR Parcubacteria Wolf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8avn | ||||||||||||
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Title | Mutant of Superoxide dismutase SodFM1 from CPR Parcubacteria Wolfebacteria | ||||||||||||
Components | Superoxide dismutase | ||||||||||||
Keywords | OXIDOREDUCTASE / Superoxide dismutase (SOD). Oxidoreductase. Iron. Bacterial. Metalloenzyme. | ||||||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Candidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||
Authors | Basle, A. / Barwinska-Sendra, A. / Sendra, K.M. / Waldron, K. | ||||||||||||
Funding support | United States, United Kingdom, 2items
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Citation | Journal: Nat Ecol Evol / Year: 2023 Title: An ancient metalloenzyme evolves through metal preference modulation. Authors: Sendra, K.M. / Barwinska-Sendra, A. / Mackenzie, E.S. / Basle, A. / Kehl-Fie, T.E. / Waldron, K.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8avn.cif.gz | 432.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8avn.ent.gz | 269.8 KB | Display | PDB format |
PDBx/mmJSON format | 8avn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/8avn ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avn | HTTPS FTP |
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-Related structure data
Related structure data | 8avkC 8avlC 8avmC 1gv3S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 203 / Label seq-ID: 2 - 203
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 23440.334 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0G1X6V3 #2: Chemical | #3: 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: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium chloride, 100 mM sodium acetate pH 5.0 and 20 % w/v polyethylene glycol 6000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→45.79 Å / Num. obs: 43267 / % possible obs: 98.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2095 / CC1/2: 0.556 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GV3 Resolution: 1.65→45.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.96 / SU B: 8.241 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.109 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.887 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→45.79 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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