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Open data
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Basic information
Entry | Database: PDB / ID: 8p14 | |||||||||
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Title | USP28 USP domain in complex with Vismodegib | |||||||||
![]() | Ubiquitin carboxyl-terminal hydrolase 28 | |||||||||
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Function / homology | ![]() protein deubiquitination involved in ubiquitin-dependent protein catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sauer, F. / Karal Nair, R. / Kisker, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: USP28 USP domain in complex with Vismodegib Authors: Sauer, F. / Karal Nair, R. / Kisker, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6h4iS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44026.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UCID oligomerization domain replaced by a linker,UCID oligomerization domain replaced by a linker Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-VIS / ![]() | ||||
#3: Chemical | ChemComp-CL / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.99 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M NaCl 0.1 M Li2SO4 0.1 M MES pH 6.4 14% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.57→47.97 Å / Num. obs: 44538 / % possible obs: 99.9 % / Redundancy: 19.1 % / CC1/2: 0.999 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.57→2.68 Å / Num. unique obs: 2825 / CC1/2: 0.402 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6H4I Resolution: 2.57→44.46 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 24.94 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→44.46 Å
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Refine LS restraints |
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LS refinement shell |
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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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