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- PDB-7rts: Crystal structure of the TIR domain from the grapevine disease re... -

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Basic information

Entry
Database: PDB / ID: 7rts
TitleCrystal structure of the TIR domain from the grapevine disease resistance protein RUN1 without the AE interface
ComponentsDisease resistance protein RUN1
KeywordsSIGNALING PROTEIN / NAD+ Hydrolase / Signalling Protein / TIR domain / NAD+ nucleosidase activity
Function / homology
Function and homology information


NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction ...NADP+ nucleosidase activity / NAD catabolic process / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleosidase activity, 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
C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance ...C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disease resistance protein RUN1
Similarity search - Component
Biological speciesVitis rotundifolia (fox grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsBurdett, H. / Kobe, B.
Funding support2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160102244
Australian Research Council (ARC)DP190102526
CitationJournal: Biorxiv / Year: 2021
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
DepositionAug 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0985
Polymers20,7131
Non-polymers3844
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.370, 50.370, 120.313
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Disease resistance protein RUN1 / NAD(+) hydrolase RUN1 / NADP(+) hydrolase RUN1 / Resistance to Uncinula necator protein / MrRUN1


Mass: 20713.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (fox grape) / Gene: RUN1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: V9M398, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o0w

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
RfactorNum. reflection% reflection
Rfree0.229 853 5.12 %
Rwork0.1975 15792 -
obs0.1991 16645 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.37 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 20 54 1407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641396
X-RAY DIFFRACTIONf_angle_d0.74481885
X-RAY DIFFRACTIONf_chiral_restr0.0515195
X-RAY DIFFRACTIONf_plane_restr0.0087242
X-RAY DIFFRACTIONf_dihedral_angle_d26.3989185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.850.36031490.26592536X-RAY DIFFRACTION99.48
1.85-1.990.26861390.20522563X-RAY DIFFRACTION99.78
1.99-2.190.25921400.19572595X-RAY DIFFRACTION99.78
2.19-2.510.23811520.19592601X-RAY DIFFRACTION99.96
2.51-3.160.2141260.21072677X-RAY DIFFRACTION100
3.16-46.460.2051470.18472820X-RAY DIFFRACTION99.97

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