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Yorodumi- PDB-3ce1: Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ce1 | ||||||
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Title | Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptococcus liquefaciens Strain N6 | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / Greek-key beta barrel / Antioxidant / Copper / Metal-binding / Zinc | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Cryptococcus liquefaciens (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Teh, A.H. / Kanamasa, S. / Kajiwara, S. / Kumasaka, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Structure of Cu/Zn superoxide dismutase from the heavy-metal-tolerant yeast Cryptococcus liquefaciens strain N6. Authors: Teh, A.H. / Kanamasa, S. / Kajiwara, S. / Kumasaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ce1.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ce1.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ce1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3ce1 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3ce1 | HTTPS FTP |
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-Related structure data
Related structure data | 1f1gS S: Starting model for refinement |
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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: 17297.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptococcus liquefaciens (fungus) / Strain: N6 / Gene: C-SOD1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0ZPR9, superoxide dismutase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-CU / |
#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: 2.04 Å3/Da / Density % sol: 39.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.2M sodium acetate, 0.1M Tris-Cl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2004 / Details: KB MIRRORS |
Radiation | Monochromator: Si 111 double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→70.53 Å / Num. all: 44741 / Num. obs: 44741 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4372 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F1G Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.864 / SU ML: 0.018 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: THE OCCUPANCY FOR DISORDERED ATOMS WAS SET TO 0.01
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.769 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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