+Open data
-Basic information
Entry | Database: PDB / ID: 3g50 | ||||||
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Title | Crystal Structure of NiSOD D3A mutant at 1.9 A | ||||||
Components | Superoxide dismutase [Ni] | ||||||
Keywords | OXIDOREDUCTASE / Nickel / Hexamer / Superoxide dismutase / NiSOD / SOD / Antioxidant / Metal-binding | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Garman, S.C. / Guce, A.I. / Herbst, R.W. / Bryngelson, P.A. / Cabelli, D.E. / Higgins, K.A. / Ryan, K.C. / Maroney, M.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution Authors: Herbst, R.W. / Guce, A. / Bryngelson, P.A. / Higgins, K.A. / Ryan, K.C. / Cabelli, D.E. / Garman, S.C. / Maroney, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g50.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g50.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g50_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 3g50_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 3g50_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3g50_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g50 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g50 | HTTPS FTP |
-Related 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: 13178.955 Da / Num. of mol.: 3 / Fragment: NiSOD (UNP residues 15 to 131) / Mutation: D3A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: 2SC7G11.16c, SCO5254, sod1, sodN / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P80735, 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: PEG 550 MME, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å |
Detector | Type: ADSC / Detector: CCD / Date: Aug 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH WITH ANOMALOUS / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→21.57 Å / Num. obs: 29881 / % possible obs: 99.9 % / Redundancy: 8 % / Rsym value: 0.046 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.929 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.493 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / 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: 37.978 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→21.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.952 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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