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Yorodumi- PDB-3l9y: Crystal structures of holo and Cu-deficient Cu/ZnSOD from the sil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l9y | ||||||
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Title | Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and the implications in Amyotrophic lateral sclerosis | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / Greek-key-barrel / Antioxidant / Copper / Cytoplasm / Metal-binding | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / copper ion binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhang, N.-N. / He, Y.-X. / Li, W.-F. / Zhao, F. / Yan, L.-F. / Zhang, G.-Z. / Teng, Y.-B. / Yu, J. / Chen, Y. / Zhou, C.-Z. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Crystal structures of holo and Cu-deficient Cu/Zn-SOD from the silkworm Bombyx mori and the implications in amyotrophic lateral sclerosis. Authors: Zhang, N.N. / He, Y.X. / Li, W.F. / Teng, Y.B. / Yu, J. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l9y.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l9y.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9y ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9y | HTTPS FTP |
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-Related structure data
Related structure data | 3l9eC 1azvS 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:
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-Components
#1: Protein | Mass: 15822.560 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Strain: P50 / Gene: SOD1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P82205, superoxide dismutase #2: Chemical | #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.0M (NH4)2SO4, 0.1M Tris-HCl, pH 8.5, 10% glycerol, 1mM CuCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 26262 / % possible obs: 99.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2560 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AZV Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.037 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.479 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 41 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.803→1.85 Å / Total num. of bins used: 20
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