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Open data
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Basic information
Entry | Database: PDB / ID: 3kbe | ||||||
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Title | Metal-free C. elegans Cu,Zn Superoxide Dismutase | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Detoxification of Reactive Oxygen Species / Platelet degranulation / regulation of vulval development / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pakhomova, O.N. / Taylor, A.B. / Schuermann, J.P. / Culotta, V.L. / Hart, P.J. | ||||||
![]() | ![]() Title: X-ray Crystal Structure of C. elegans Cu,Zn Superoxide Dismutase Authors: Pakhomova, O.N. / Taylor, A.B. / Schuermann, J.P. / Culotta, V.L. / Hart, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 61.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kbfC ![]() 2c9vS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 16126.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100 mM bicine, 2.4 M ammonium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.1→30 Å / Num. obs: 59043 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.1 Å2 / Rsym value: 0.035 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 5381 / Rsym value: 0.3 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 2C9V Resolution: 1.1→24.44 Å / SU ML: 0.63 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.851 Å2 / ksol: 0.448 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→24.44 Å
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Refine LS restraints |
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LS refinement shell |
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