+Open data
-Basic information
Entry | Database: PDB / ID: 5n57 | |||||||||
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Title | Staphylococcus aureus cambialistic superoxide dismutase SodM | |||||||||
Components | Superoxide dismutase | |||||||||
Keywords | OXIDOREDUCTASE / superoxide dismutase / cambialistic / Staphylococcus aureus | |||||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Barwinska-Sendra, A. / Basle, A. / Waldron, K. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Phys Chem Chem Phys / Year: 2018 Title: A charge polarization model for the metal-specific activity of superoxide dismutases. Authors: Barwinska-Sendra, A. / Basle, A. / Waldron, K.J. / Un, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n57.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n57.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 5n57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n57_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 5n57_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 5n57_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5n57_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/5n57 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n57 | HTTPS FTP |
-Related structure data
Related structure data | 5n56C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 199 / Label seq-ID: 2 - 199
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-Components
#1: Protein | Mass: 23067.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: sodA, sodM, A4U86_04870, BN1321_40056, ERS072738_00830, ERS072840_00559, ERS073147_02394, ERS073767_02269, ERS074020_00889, ERS1058648_00955, FORC27_0128, HMPREF3211_00238, SAMEA2298760_02426 Production host: Escherichia coli (E. coli) References: UniProt: W8UU58, UniProt: Q2G261*PLUS, superoxide dismutase #2: Chemical | #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 | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.05 M KSCN, 34 % PEG 2K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.282 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.55 Å / Num. obs: 24136 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.968 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.3 % / Num. unique obs: 2339 / CC1/2: 0.76 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCV Resolution: 2.3→46.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.214 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.213 / 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: 43.636 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→46.55 Å
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Refine LS restraints |
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