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- PDB-5h3c: Crystal structure of Arabidopsis SNC1 TIR domain -

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Basic information

Entry
Database: PDB / ID: 5h3c
TitleCrystal structure of Arabidopsis SNC1 TIR domain
ComponentsProtein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
KeywordsIMMUNE SYSTEM / Plant / Immunity / Rprotein
Function / homology
Function and homology information


systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / intracellular membrane-bounded organelle / nucleotide binding / endoplasmic reticulum ...systemic acquired resistance, salicylic acid mediated signaling pathway / response to auxin / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / ADP binding / defense response to bacterium / intracellular membrane-bounded organelle / nucleotide binding / endoplasmic reticulum / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain ...Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Toll/interleukin-1 receptor homology (TIR) domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / 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 domain superfamily / Winged helix DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.596 Å
AuthorsHyun, K.G. / Yoon, J.M. / Song, J.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRF2016R1A2B3006293,2014R1A1A1004807 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of Arabidopsis thaliana SNC1 TIR domain
Authors: Hyun, K.G. / Lee, Y. / Yoon, J. / Yi, H. / Song, J.J.
History
DepositionOct 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1
B: Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1


Theoretical massNumber of molelcules
Total (without water)40,0682
Polymers40,0682
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint2 kcal/mol
Surface area15040 Å2
Unit cell
Length a, b, c (Å)81.534, 81.534, 125.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein SUPPRESSOR OF npr1-1, CONSTITUTIVE 1 / AtSNC1 / Disease resistance RPP5-like protein


Mass: 20034.160 Da / Num. of mol.: 2 / Fragment: UNP residues 17-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNC1, BAL, At4g16890, dl4475c, FCAALL.51 / Production host: Escherichia coli (E. coli) / References: UniProt: O23530
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.3M Ammonium acetate, 35% PEG 3350, 0.1M HEPES pH 7.5, 6% Glycerol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13649 / % possible obs: 99.2 % / Redundancy: 6.8 % / Net I/σ(I): 16.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.596→37.331 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2779 1341 9.95 %
Rwork0.2192 --
obs0.2249 13478 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.596→37.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 0 30 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092487
X-RAY DIFFRACTIONf_angle_d1.0323345
X-RAY DIFFRACTIONf_dihedral_angle_d3.5591505
X-RAY DIFFRACTIONf_chiral_restr0.056372
X-RAY DIFFRACTIONf_plane_restr0.005420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.596-2.68880.32191280.2581150X-RAY DIFFRACTION95
2.6888-2.79640.35861260.26891148X-RAY DIFFRACTION95
2.7964-2.92360.36011280.28091172X-RAY DIFFRACTION97
2.9236-3.07770.39751290.27271182X-RAY DIFFRACTION98
3.0777-3.27040.29281340.24991208X-RAY DIFFRACTION99
3.2704-3.52270.29991340.2221210X-RAY DIFFRACTION99
3.5227-3.87690.28221370.20481230X-RAY DIFFRACTION99
3.8769-4.43710.23581360.19951234X-RAY DIFFRACTION100
4.4371-5.58730.22571390.18231252X-RAY DIFFRACTION100
5.5873-37.33470.24661500.20981351X-RAY DIFFRACTION99

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