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- PDB-7x8u: Crystal structure of the N-terminal Solanaceae domain of the Sw-5... -

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Basic information

Entry
Database: PDB / ID: 7x8u
TitleCrystal structure of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor
ComponentsTospovirus resistance protein B
KeywordsPLANT PROTEIN / Solanaceae domain / coiled-coil / immune receptor
Function / homology
Function and homology information


plant-type hypersensitive response / ADP binding / membrane / cytoplasm
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tospovirus resistance protein B
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å
AuthorsLi, J. / Xin, J. / Xing, W. / Tao, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170162 China
National Natural Science Foundation of China (NSFC)31630062 China
CitationJournal: To Be Published
Title: Crystal structure of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor
Authors: Li, J. / Xin, J. / Xing, W. / Tao, X.
History
DepositionMar 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tospovirus resistance protein B


Theoretical massNumber of molelcules
Total (without water)29,3201
Polymers29,3201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13620 Å2
Unit cell
Length a, b, c (Å)81.530, 81.530, 98.445
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)

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Components

#1: Protein Tospovirus resistance protein B / Sw-5b NLR immune receptor


Mass: 29319.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Sw5-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q941Q8

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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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 0.1 M Tris-HCl pH 7.8, 2.6% gamma-PGA (Na+ form, LM), 2.4% w/v PEG20000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.76→40.49 Å / Num. obs: 9900 / % possible obs: 99.9 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 19.1
Reflection shellResolution: 2.76→2.91 Å / Rmerge(I) obs: 1.471 / Num. unique obs: 1438 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.89→31.4 Å / SU ML: 0.3169 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 856 10.09 %
Rwork0.2488 7631 -
obs0.2507 8487 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.12 Å2
Refinement stepCycle: LAST / Resolution: 2.89→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 0 0 1903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061935
X-RAY DIFFRACTIONf_angle_d0.78942593
X-RAY DIFFRACTIONf_chiral_restr0.0494290
X-RAY DIFFRACTIONf_plane_restr0.0036325
X-RAY DIFFRACTIONf_dihedral_angle_d14.9239749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.080.29081380.32541254X-RAY DIFFRACTION98.65
3.08-3.310.35851400.29881239X-RAY DIFFRACTION99.57
3.31-3.650.30211450.30791278X-RAY DIFFRACTION99.93
3.65-4.170.26371430.25621261X-RAY DIFFRACTION99.86
4.18-5.250.25041420.23521287X-RAY DIFFRACTION100
5.26-31.40.24571480.21371312X-RAY DIFFRACTION99.18

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