+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yk8 | ||||||
---|---|---|---|---|---|---|---|
Title | OTU-like deubiquitinase from Legionella -Lpg2529 | ||||||
![]() | Uncharacterized protein | ||||||
![]() | CELL INVASION / deubiquitinase / legionella / OTU / effector protein | ||||||
Function / homology | : / Dot/Icm T4SS effector![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, D. / Dikic, I. | ||||||
![]() | ![]() Title: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. Authors: Shin, D. / Bhattacharya, A. / Cheng, Y.L. / Alonso, M.C. / Mehdipour, A.R. / van der Heden van Noort, G.J. / Ovaa, H. / Hummer, G. / Dikic, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34752.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2529 / Production host: ![]() ![]() #2: Chemical | ChemComp-PT / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % PEG3350, 100 mM Tris-HCl pH 8.5, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.070333 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→44.53 Å / Num. obs: 23185 / % possible obs: 99.23 % / Redundancy: 2 % / Biso Wilson estimate: 61.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03065 / Net I/σ(I): 14.85 |
Reflection shell | Resolution: 2.42→2.506 Å / Rmerge(I) obs: 0.3765 / Num. unique obs: 2278 / CC1/2: 0.811 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→44.53 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|