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- PDB-6s2p: Structure of the NB-ARC domain from the Tomato immune receptor NRC1 -

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Basic information

Entry
Database: PDB / ID: 6s2p
TitleStructure of the NB-ARC domain from the Tomato immune receptor NRC1
ComponentsNRC1
KeywordsPLANT PROTEIN / NLR receptor / NB-ARC domain / plant immunity
Function / homology
Function and homology information


defense response to other organism / ADP binding / defense response
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal 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
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein / NRC1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSteele, J.F.C. / Banfield, M.J.
Citation
Journal: Plos One / Year: 2019
Title: Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor.
Authors: Steele, J.F.C. / Hughes, R.K. / Banfield, M.J.
#1: Journal: Biorxiv / Year: 2019
Title: Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor
Authors: Steele, J.F.C. / Hughes, R.K. / Banfield, M.J.
History
DepositionJun 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: NRC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5782
Polymers40,1511
Non-polymers4271
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.517, 110.517, 53.338
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein NRC1


Mass: 40151.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: A1X877, UniProt: A0A3Q7EK40*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 8% PEG 1500, 0.1 M MMT (MES, malic acid and Tris,)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13066 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1463 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.855 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0.62 / Phase error: 42.23
RfactorNum. reflection% reflection
Rfree0.3367 1208 4.79 %
Rwork0.305 --
obs0.3067 25214 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.59 Å2 / Biso mean: 83.3549 Å2 / Biso min: 36.9 Å2
Refinement stepCycle: final / Resolution: 2.5→47.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 27 0 2081
Biso mean--62.35 --
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5002-2.60030.44981280.401326652793
2.6003-2.71860.43731300.367426682798
2.7186-2.86190.421380.352426852823
2.8619-3.04120.44881010.34826992800
3.0412-3.2760.40391340.333926542788
3.276-3.60550.33651140.327127092823
3.6055-4.1270.34932160.314325772793
4.127-5.19860.30741210.264726762797
5.1986-47.8640.26871260.282826732799

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