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- PDB-2qkw: Structural basis for activation of plant immunity by bacterial ef... -

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Basic information

Entry
Database: PDB / ID: 2qkw
TitleStructural basis for activation of plant immunity by bacterial effector protein AvrPto
Components
  • Avirulence protein
  • Protein kinase
KeywordsTRANSFERASE / three-helix bundle motif / Avrpto-pto duplex / layered beta-sheets / Kinase / Serine/threonine-protein kinase
Function / homology
Function and homology information


plasmodesma / transmembrane receptor protein tyrosine kinase activity / phosphorylation / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
AvrPto / Type III secretion system, AvrPto / AvrPto superfamily / Central core of the bacterial effector protein AvrPto / Receptor-like protein kinase ANXUR1-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...AvrPto / Type III secretion system, AvrPto / AvrPto superfamily / Central core of the bacterial effector protein AvrPto / Receptor-like protein kinase ANXUR1-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Avirulence protein / Protein kinase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
Solanum pimpinellifolium (currant tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsXing, W.M. / Zou, Y. / Liu, Q. / Hao, Q. / Zhou, J.M. / Chai, J.J.
CitationJournal: Nature / Year: 2007
Title: The structural basis for activation of plant immunity by bacterial effector protein AvrPto
Authors: Xing, W. / Zou, Y. / Liu, Q. / Liu, J. / Luo, X. / Huang, Q. / Chen, S. / Zhu, L. / Bi, R. / Hao, Q. / Wu, J.W. / Zhou, J.M. / Chai, J.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avirulence protein
B: Protein kinase


Theoretical massNumber of molelcules
Total (without water)54,8442
Polymers54,8442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.465, 94.591, 98.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe functional unit is a heterodimer containing one AvrPto molecule and one Pto molecule in the asymmetric unit.

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Components

#1: Protein Avirulence protein


Mass: 18284.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: avrP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08242
#2: Protein Protein kinase / Pto disease resistance protein / Serine/threonine protein kinase Pto / Pto kinase


Mass: 36559.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum pimpinellifolium (currant tomato)
Gene: Pto / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q40234, non-specific serine/threonine protein kinase

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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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.55M potassium sodium tartrate, 0.1M hepes pH 7.5, 10 mM taurine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9794, 0.9797, 0.9
ROTATING ANODERIGAKU MICROMAX-00721.5418
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMar 28, 2005
RIGAKU RAXIS IV2IMAGE PLATEMar 21, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystalMADMx-ray1
2NI FILTERSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97971
30.91
41.54181
ReflectionResolution: 3→100 Å / Num. all: 15185 / Num. obs: 14608 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.6
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.67 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.885 / SU B: 56.783 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.538 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30337 815 6.9 %RANDOM
Rwork0.27131 ---
all0.27364 11252 --
obs0.27364 10933 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.291 Å2
Baniso -1Baniso -2Baniso -3
1--4.71 Å20 Å20 Å2
2--3.82 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 0 0 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213197
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9624321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77323.91156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04315.026572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9241525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022412
X-RAY DIFFRACTIONr_nbd_refined0.2070.21480
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.24
X-RAY DIFFRACTIONr_mcbond_it0.3341.52012
X-RAY DIFFRACTIONr_mcangle_it0.59723149
X-RAY DIFFRACTIONr_scbond_it0.59131324
X-RAY DIFFRACTIONr_scangle_it1.0334.51172
LS refinement shellResolution: 3.2→3.368 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.417 118 -
Rwork0.304 1534 -
obs--98.04 %

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