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- PDB-7rts: Crystal structure of the TIR domain from the grapevine disease re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rts | |||||||||
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Title | Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1 without the AE interface | |||||||||
![]() | Disease resistance protein RUN1 | |||||||||
![]() | SIGNALING PROTEIN / NAD+ Hydrolase / Signalling Protein / TIR domain / NAD+ nucleosidase activity | |||||||||
Function / homology | ![]() NAD catabolic process / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction ...NAD catabolic process / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Burdett, H. / Kobe, B. | |||||||||
Funding support | 2items
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![]() | ![]() Title: Self-association configures the NAD + -binding site of plant NLR TIR domains Authors: Burdett, H. / Hu, X. / Rank, M.X. / Maruta, N. / Kobe, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rx1C ![]() 7s2zC ![]() 6o0wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 20713.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: V9M398, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate pH 4.6, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.739→46.46 Å / Num. obs: 16661 / % possible obs: 99.83 % / Redundancy: 25.8 % / Biso Wilson estimate: 25.66 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04796 / Rrim(I) all: 0.04894 / Net I/σ(I): 41.33 |
Reflection shell | Resolution: 1.739→1.801 Å / Rmerge(I) obs: 0.4933 / Mean I/σ(I) obs: 6.04 / Num. unique obs: 1600 / CC1/2: 0.978 / CC star: 0.994 / Rrim(I) all: 0.5029 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6o0w Resolution: 1.74→46.46 Å / SU ML: 0.2524 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6267 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: 30.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→46.46 Å
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Refine LS restraints |
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LS refinement shell |
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