+Open data
-Basic information
Entry | Database: PDB / ID: 3bfr | ||||||
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Title | The crystal structure of Sod2 from Saccharomyces cerevisiae | ||||||
Components | Superoxide dismutase [Mn] | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta fold / Manganese / Metal-binding / Mitochondrion / Transit peptide | ||||||
Function / homology | Function and homology information Detoxification of Reactive Oxygen Species / superoxide dismutase / superoxide dismutase activity / reactive oxygen species metabolic process / manganese ion binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | He, Y.-X. / Zhao, M.-X. / Zhou, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structures of native and Fe-substituted SOD2 from Saccharomyces cerevisiae Authors: Kang, Y. / He, Y.-X. / Zhao, M.-X. / Li, W.-F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bfr.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfr.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfr ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfr | HTTPS FTP |
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-Related structure data
Related structure data | 3rn4C 1kkcS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24125.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: s288c / Gene: SOD2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta / References: UniProt: P00447, superoxide dismutase |
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#2: Chemical | ChemComp-MN3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 Details: 50% MPD, 0.2M NH4H2PO4,0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→18.55 Å / Num. obs: 16963 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KKC Resolution: 2.05→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.729 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.061 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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