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Open data
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Basic information
Entry | Database: PDB / ID: 8txf | ||||||
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Title | AvrB bound with RIN4 C-NOI motif | ||||||
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![]() | TRANSFERASE / Protein complex | ||||||
Function / homology | Avirulence B/C / Avirulence B/C superfamily / Avirulence protein / extracellular region / Avirulence protein B![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, W. / Orth, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.1 KB | Display | ![]() |
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PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.3 KB | Display | ![]() |
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Full document | ![]() | 469.6 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8twjC ![]() 8twoC ![]() 8twsC C: citing same article ( |
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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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36262.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#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-EDO / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50 Å / Num. obs: 82030 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 13.57 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 46.1 |
Reflection shell | Resolution: 1.29→1.34 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 7654 / CC1/2: 0.91 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→36.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.8328536441 Å / Origin y: 23.1880264633 Å / Origin z: -11.8653070889 Å
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Refinement TLS group | Selection details: all |