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Open data
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Basic information
Entry | Database: PDB / ID: 4emo | ||||||
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Title | Crystal structure of the PH domain of SHARPIN | ||||||
![]() | Sharpin![]() | ||||||
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Function / homology | ![]() apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K. | ||||||
![]() | ![]() Title: Structural Analysis of SHARPIN, a Subunit of a Large Multi-protein E3 Ubiquitin Ligase, Reveals a Novel Dimerization Function for the Pleckstrin Homology Superfold. Authors: Stieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 13355.524 Da / Num. of mol.: 4 / Mutation: L21M, L101M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.72 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 4M sodium formate, pH 7.4, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: May 29, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.9 % / Av σ(I) over netI: 17.17 / Number: 213897 / Rmerge(I) obs: 0.071 / Χ2: 0.95 / D res high: 2 Å / D res low: 30 Å / Num. obs: 55100 / % possible obs: 99.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→30 Å / Num. obs: 29888 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.071 / Χ2: 0.949 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.73 / FOM acentric: 0.76 / FOM centric: 0.62 / Reflection: 17560 / Reflection acentric: 14320 / Reflection centric: 3240 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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 max: 94.58 Å2 / Biso mean: 34.5554 Å2 / Biso min: 14.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.048 Å / Total num. of bins used: 20
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