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- PDB-7rx1: Crystal structure of the TIR domain from the grapevine disease re... -

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Basic information

Entry
Database: PDB / ID: 7rx1
TitleCrystal structure of the TIR domain from the grapevine disease resistance protein RUN1
ComponentsDisease resistance protein RUN1
KeywordsSIGNALING PROTEIN / NAD+ Hydrolase / Signalling Protein / TIR domain / NAD+ nucleosidase activity
Function / homology
Function and homology information


NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / positive regulation of programmed cell death / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / defense response to fungus / ADP binding / signal transduction ...NAD catabolic process / NAD+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / 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 / NB-ARC / NB-ARC domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Toll - interleukin 1 - resistance ...C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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: 1.89 Å
AuthorsBurdett, H. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
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 21, 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
B: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0999
Polymers41,4272
Non-polymers6727
Water2,072115
1
A: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0024
Polymers20,7131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disease resistance protein RUN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0985
Polymers20,7131
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.435, 41.471, 77.232
Angle α, β, γ (deg.)90.000, 118.514, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis rotundifolia (fox grape) / Gene: RUN1 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Lithium Sulfate, 0.1 M HEPES pH 7, 20% PEG3350

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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: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→33.93 Å / Num. obs: 34128 / % possible obs: 99.48 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.67 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Net I/σ(I): 12.06
Reflection shellResolution: 1.892→1.959 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3294 / CC1/2: 0.358 / CC star: 0.726 / Rpim(I) all: 0.801 / Rrim(I) all: 0.074 / % possible all: 97.6

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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: 1.89→33.93 Å / SU ML: 0.2515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 1627 4.77 %
Rwork0.2008 32491 -
obs0.202 34118 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.53 Å2
Refinement stepCycle: LAST / Resolution: 1.89→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 35 115 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792924
X-RAY DIFFRACTIONf_angle_d0.80723938
X-RAY DIFFRACTIONf_chiral_restr0.0521402
X-RAY DIFFRACTIONf_plane_restr0.0077508
X-RAY DIFFRACTIONf_dihedral_angle_d28.9654390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.950.35371230.31912600X-RAY DIFFRACTION97.11
1.95-2.010.33031320.29322694X-RAY DIFFRACTION99.86
2.01-2.080.28571400.27392718X-RAY DIFFRACTION99.9
2.08-2.170.33131210.2632663X-RAY DIFFRACTION99.82
2.17-2.260.28751300.23742720X-RAY DIFFRACTION99.75
2.26-2.380.28611360.22982708X-RAY DIFFRACTION99.82
2.38-2.530.29331560.2242682X-RAY DIFFRACTION99.89
2.53-2.730.24411330.22592716X-RAY DIFFRACTION99.79
2.73-30.26381420.23212707X-RAY DIFFRACTION99.75
3-3.440.22691290.21652734X-RAY DIFFRACTION99.62
3.44-4.330.18731330.16862749X-RAY DIFFRACTION99.59
4.33-33.930.16261520.14682800X-RAY DIFFRACTION99.19

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