+Open data
-Basic information
Entry | Database: PDB / ID: 6qzn | ||||||
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Title | H30 MnSOD-3 Mutant III | ||||||
Components | (Superoxide dismutase [Mn] 2, mitochondrial) x 2 | ||||||
Keywords | OXIDOREDUCTASE / superoxide / mutation / dismutase | ||||||
Function / homology | Function and homology information mitochondrial respirasome / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / manganese ion binding / protein homodimerization activity / mitochondrion Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Bonetta, R. / Trinh, C.H. / Hunter, G.J. / Hunter, T. | ||||||
Citation | Journal: To Be Published Title: H30 MnSOD-3 Mutant II Authors: Bonetta, R. / Trinh, C.H. / Hunter, G.J. / Hunter, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qzn.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qzn.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/6qzn ftp://data.pdbj.org/pub/pdb/validation_reports/qz/6qzn | HTTPS FTP |
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-Related structure data
Related structure data | 6qzmC 6s0dC 3dc5S 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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-Components
#1: Protein | Mass: 22234.266 Da / Num. of mol.: 1 / Mutation: H30Q Source method: isolated from a genetically manipulated source Details: Residue 128 is S-hydroxycysteine instead of cysteine Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sod-3, C08A9.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41977, superoxide dismutase | ||||
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#2: Protein | Mass: 22365.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residue 128 is S-hydroxycysteine instead of cysteine Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sod-3, C08A9.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41977, superoxide dismutase | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: bicine ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.09 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→57.91 Å / Num. obs: 57915 / % possible obs: 99.9 % / Redundancy: 9.3 % / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.64→1.73 Å / Num. unique obs: 3988 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dc5 Resolution: 1.64→57.91 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.779 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / 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: 36.498 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→57.91 Å
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Refine LS restraints |
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