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- PDB-3hgk: crystal structure of effect protein AvrptoB complexed with kinase Pto -

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Basic information

Entry
Database: PDB / ID: 3hgk
Titlecrystal structure of effect protein AvrptoB complexed with kinase Pto
Components
  • Effector protein hopAB2
  • Protein kinase
KeywordsTRANSFERASE / five helices / Pto P+1 loop / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Hypersensitive response elicitation / Ligase / Secreted / Ubl conjugation / Ubl conjugation pathway / Virulence
Function / homology
Function and homology information


effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host programmed cell death / plasmodesma / Transferases; Acyltransferases; Aminoacyltransferases / transmembrane receptor protein tyrosine kinase activity / transferase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Monooxygenase - #110 / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Receptor-like protein kinase ANXUR1-like / Monooxygenase ...Monooxygenase - #110 / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Receptor-like protein kinase ANXUR1-like / Monooxygenase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Protein kinase / Effector protein HopAB2
Similarity search - Component
Biological speciesSolanum pimpinellifolium (currant tomato)
Pseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDong, J. / Fan, F. / Gu, L. / Chai, J.
CitationJournal: Plant Cell / Year: 2009
Title: Crystal Structure of the Complex between Pseudomonas Effector AvrPtoB and the Tomato Pto Kinase Reveals Both a Shared and a Unique Interface Compared with AvrPto-Pto
Authors: Dong, J. / Xiao, F. / Fan, F. / Gu, L. / Cang, H. / Martin, G.B. / Chai, J.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase
B: Protein kinase
C: Protein kinase
D: Protein kinase
E: Effector protein hopAB2
F: Effector protein hopAB2
G: Effector protein hopAB2
H: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)187,0368
Polymers187,0368
Non-polymers00
Water00
1
A: Protein kinase
F: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)46,7592
Polymers46,7592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area18410 Å2
MethodPISA
2
B: Protein kinase
E: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)46,7592
Polymers46,7592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-11 kcal/mol
Surface area18080 Å2
MethodPISA
3
C: Protein kinase
G: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)46,7592
Polymers46,7592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-12 kcal/mol
Surface area17880 Å2
MethodPISA
4
D: Protein kinase
H: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)46,7592
Polymers46,7592
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-12 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.070, 104.470, 298.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein kinase / Pto / Pto disease resistance protein / Pto kinase / Serine/threonine protein kinase Pto


Mass: 37330.395 Da / Num. of mol.: 4 / Mutation: D193G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum pimpinellifolium (currant tomato)
Gene: Pto / Plasmid: PET-30A / Production host: Escherichia coli (E. coli) / References: UniProt: Q40234
#2: Protein
Effector protein hopAB2 / AvrPtoB / Avirulence protein avrPtoB / E3 ubiquitin-protein ligase


Mass: 9428.645 Da / Num. of mol.: 4 / Fragment: UNP residues 121-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: hopAB2, avrPtoB, PSPTO_3087 / Species (production host): plasmid / Production host: Escherichia coli (E. coli) / Tissue fraction (production host): PGEX-6P-1
References: UniProt: Q8RSY1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1M tri-Sodium Citrate dihydrate, 17.5% (w/v) Polyethylene Glycol 3350, 0.1mM Tris-HCl pH 7.9, 10.0mM phenol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 7, 2008
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→99 Å / Num. obs: 29886 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.3
Reflection shellResolution: 3.3→3.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3HGL for AvrPtoB AND 2QKW for Pto

3hgl

2qkw


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 120.055 / SU ML: 0.79 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.714 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3305 1506 5.1 %RANDOM
Rwork0.31706 ---
obs0.31775 28059 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 119.92 Å2 / Biso mean: 81.806 Å2 / Biso min: 44.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.99 Å20 Å20 Å2
2--14.94 Å20 Å2
3----8.95 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11599 0 0 0 11599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02111823
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96115960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64151450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.74623.611576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92915.0282124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.83215100
X-RAY DIFFRACTIONr_chiral_restr0.0890.21763
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028912
X-RAY DIFFRACTIONr_nbd_refined0.2720.26563
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.2123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.24
X-RAY DIFFRACTIONr_mcbond_it2.4851.57457
X-RAY DIFFRACTIONr_mcangle_it3.856211635
X-RAY DIFFRACTIONr_scbond_it1.72534856
X-RAY DIFFRACTIONr_scangle_it2.4014.54325
LS refinement shellResolution: 3.297→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 94 -
Rwork0.482 1976 -
all-2070 -
obs--98.15 %

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