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- PDB-5teb: Crystal Structure of the TIR domain from the Arabidopsis Thaliana... -

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Basic information

Entry
Database: PDB / ID: 5teb
TitleCrystal Structure of the TIR domain from the Arabidopsis Thaliana disease resistance protein RPP1
ComponentsRecognition of Peronospora parasitica 1
KeywordsSIGNALING PROTEIN / TIR domain / flavodoxin-like / resistance protein / signaling domain
Function / homology
Function and homology information


ADP binding / defense response / hydrolase activity / signal transduction
Similarity search - Function
Toll/interleukin-1 receptor homology (TIR) 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 ...Toll/interleukin-1 receptor homology (TIR) 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Recognition of Peronospora parasitica 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsBentham, A.R. / Zhang, X. / Croll, T. / Williams, S. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120100685 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Multiple functional self-association interfaces in plant TIR domains.
Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / ...Authors: Zhang, X. / Bernoux, M. / Bentham, A.R. / Newman, T.E. / Ve, T. / Casey, L.W. / Raaymakers, T.M. / Hu, J. / Croll, T.I. / Schreiber, K.J. / Staskawicz, B.J. / Anderson, P.A. / Sohn, K.H. / Williams, S.J. / Dodds, P.N. / Kobe, B.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recognition of Peronospora parasitica 1
B: Recognition of Peronospora parasitica 1
C: Recognition of Peronospora parasitica 1
D: Recognition of Peronospora parasitica 1
E: Recognition of Peronospora parasitica 1
F: Recognition of Peronospora parasitica 1
G: Recognition of Peronospora parasitica 1
H: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)153,6088
Polymers153,6088
Non-polymers00
Water0
1
A: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Recognition of Peronospora parasitica 1


Theoretical massNumber of molelcules
Total (without water)19,2011
Polymers19,2011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.890, 84.330, 122.750
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Recognition of Peronospora parasitica 1


Mass: 19201.025 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RPP1 / Plasmid: pMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9IW02

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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: 2.87 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 15% PEG 6000, 0.2 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.55→40.945 Å / Num. obs: 41428 / % possible obs: 99.6 % / Redundancy: 7.6 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.58→2.66 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.59 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.11rc2_2531phasing
PHENIX1.11rc2_2531refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.796→40.945 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.68 / Phase error: 29.25
RfactorNum. reflection% reflection
Rfree0.2685 1979 4.78 %
Rwork0.2179 --
obs0.2203 41414 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.796→40.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10533 0 0 0 10533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610733
X-RAY DIFFRACTIONf_angle_d0.98814413
X-RAY DIFFRACTIONf_dihedral_angle_d18.8896555
X-RAY DIFFRACTIONf_chiral_restr0.0581589
X-RAY DIFFRACTIONf_plane_restr0.0091819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7964-2.86630.3981260.33372689X-RAY DIFFRACTION96
2.8663-2.94380.36561340.29842827X-RAY DIFFRACTION100
2.9438-3.03040.32161710.29992787X-RAY DIFFRACTION100
3.0304-3.12820.33331380.28482820X-RAY DIFFRACTION100
3.1282-3.23990.32761780.26872764X-RAY DIFFRACTION100
3.2399-3.36960.28521360.2572808X-RAY DIFFRACTION100
3.3696-3.52290.28251080.22922857X-RAY DIFFRACTION100
3.5229-3.70850.26941250.22272832X-RAY DIFFRACTION100
3.7085-3.94070.2394990.2162872X-RAY DIFFRACTION100
3.9407-4.24460.2393970.19462882X-RAY DIFFRACTION100
4.2446-4.67120.21411670.17612783X-RAY DIFFRACTION100
4.6712-5.34590.29661880.18132803X-RAY DIFFRACTION100
5.3459-6.73040.2621590.20862828X-RAY DIFFRACTION100
6.7304-40.94930.22581530.19952883X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.66550.3897-3.2392.13680.29677.37920.206-0.07010.38260.2075-0.05890.1639-0.2614-0.3969-0.06770.49140.07910.11260.31980.07080.34614.80991.04830.4644
25.3227-0.3696-1.44893.8693-0.16026.7579-0.07640.25740.1016-0.1243-0.0892-0.43890.38790.04260.12670.24310.0115-0.01440.25130.03490.296411.71960.1069-33.8756
34.1954-0.4131.24272.7387-0.8837.05980.0243-0.2588-0.12690.2933-0.1369-0.38370.47580.1970.13360.30620.0165-0.04290.2333-0.0150.4042-29.5275-2.3649-61.0941
44.4855-0.96871.93372.7271-0.20465.33440.39591.0615-0.3621-0.424-0.43460.43450.4506-0.28670.15380.34580.0526-0.07960.6499-0.1570.4166-35.8861-2.013-95.304
56.95190.6532-0.68676.7723-0.32317.7093-0.42180.48290.0903-0.02840.4394-0.20210.2147-0.327-0.08350.3527-0.0423-0.00070.3537-0.16450.4015-61.3969-2.6149-68.2546
65.3181-0.0468-1.10124.5392-1.16145.75640.2012-0.06870.34920.03810.0049-0.096-0.43840.4397-0.17970.2797-0.0748-0.10930.2889-0.01540.2947-4.2045-1.2569-87.8266
78.20320.46661.27684.4556-0.63997.3403-0.24650.2427-0.137-0.20430.1969-0.4428-0.23310.6940.03430.34940.10120.05780.4670.05450.332336.87170.4296-6.5038
85.2716-0.43170.4947.43730.53656.1846-0.0573-0.5538-0.1056-0.07170.15150.0131-0.241-0.3471-0.01760.332-0.11280.02650.68630.0030.3584-20.54030.7247-27.1821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'D' and resid 89 through 254)
2X-RAY DIFFRACTION2(chain 'E' and resid 89 through 254)
3X-RAY DIFFRACTION3(chain 'A' and resid 89 through 254)
4X-RAY DIFFRACTION4(chain 'B' and resid 89 through 254)
5X-RAY DIFFRACTION5(chain 'C' and resid 89 through 254)
6X-RAY DIFFRACTION6(chain 'F' and resid 89 through 254)
7X-RAY DIFFRACTION7(chain 'G' and resid 90 through 254)
8X-RAY DIFFRACTION8(chain 'H' and resid 89 through 254)

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