+
Open data
-
Basic information
Entry | Database: PDB / ID: 8two | ||||||
---|---|---|---|---|---|---|---|
Title | AvrB bound with UDP and RIN4_T166-Rha | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / Protein complex | ||||||
Function / homology | Avirulence B/C / Avirulence B/C superfamily / Avirulence protein / extracellular region / alpha-L-rhamnopyranose / URIDINE-5'-DIPHOSPHATE / Avirulence protein B![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, W. / Orth, K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4. Authors: Peng, W. / Garcia, N. / Servage, K.A. / Kohler, J.J. / Ready, J.M. / Tomchick, D.R. / Fernandez, J. / Orth, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 197.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8twjC ![]() 8twsC ![]() 8txfC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36262.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 3428.589 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-UDP / |
#4: Sugar | ChemComp-RAM / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris (pH 7.5~7.8), 27%~32% PEG 550 MME |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0358 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→52.15 Å / Num. obs: 16986 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 49.65 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.61 |
Reflection shell | Resolution: 2.09→2.13 Å / Num. unique obs: 828 / CC1/2: 0.233 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→52.15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.4834 Å / Origin y: 22.8961 Å / Origin z: 9.8324 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |