+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vij | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of USP7-HUBL domain | ||||||
![]() | Ubiquitin carboxyl-terminal hydrolase 7 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() regulation of telomere capping / monoubiquitinated protein deubiquitination / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feng, N. / Zeng, K.W. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy. Authors: Zhang, X.W. / Feng, N. / Liu, Y.C. / Guo, Q. / Wang, J.K. / Bai, Y.Z. / Ye, X.M. / Yang, Z. / Yang, H. / Liu, Y. / Yang, M.M. / Wang, Y.H. / Shi, X.M. / Liu, D. / Tu, P.F. / Zeng, K.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 123.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7xpyC ![]() 2ylmS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 61800.254 Da / Num. of mol.: 1 / Fragment: HUBL domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.85 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 2% v/v Tacsimate pH 7.0, 0.1M imidazole pH 7.0, 8% w/v polyethylene glycol 3350, 5% v/v 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→149.55 Å / Num. obs: 44009 / % possible obs: 99.4 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rrim(I) all: 0.051 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4284 / CC1/2: 0.842 / Rrim(I) all: 1.027 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 2YLM Resolution: 2.3→45.391 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 31.8 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.87 Å2 / Biso mean: 75.0186 Å2 / Biso min: 34.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→45.391 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|