+Open data
-Basic information
Entry | Database: PDB / ID: 6ex3 | |||||||||
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Title | Staphylococcus aureus superoxide dismutase SodA | |||||||||
Components | Superoxide dismutase | |||||||||
Keywords | OXIDOREDUCTASE / superoxide dismutase / cambialistic / Staphylococcus aureus / metalloenzyme | |||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Barwinska-Sendra, A. / Basle, A. / Waldron, K. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: An evolutionary path to altered cofactor specificity in a metalloenzyme Authors: Barwinska-Sendra, A. / Garcia, Y.M. / Sendra, K. / Basle, A. / Mackenzie, E.S. / Tarrant, E. / Card, P. / Tabares, L.C. / Bicep, C. / Un, S. / 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 | 6ex3.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ex3.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ex3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ex3_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 6ex3_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 6ex3_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 6ex3_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/6ex3 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6ex3 | HTTPS FTP |
-Related structure data
Related structure data | 6ex4C 6ex5C 2rcvS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22738.299 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: sodA, BER48_001496, BN1321_260190, CEJ93_06715, ERS072738_01312, ERS072840_00871, ERS073583_00205, ERS074020_01135, HMPREF3211_01704 Production host: Escherichia coli (E. coli) References: UniProt: W8TT57, UniProt: P0A0J3*PLUS, superoxide dismutase #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2 100 mM Tris pH 8.5 30% (w/v) PEG 4000 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.01 Å / Num. obs: 33834 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2914 / CC1/2: 0.749 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCV Resolution: 2.2→47.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.076 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.268 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.73 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→47.01 Å
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Refine LS restraints |
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