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- PDB-3hgk: crystal structure of effect protein AvrptoB complexed with kinase Pto -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hgk | ||||||
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Title | crystal structure of effect protein AvrptoB complexed with kinase Pto | ||||||
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![]() | TRANSFERASE / 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 | ![]() effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host defense-related programmed cell death / plasmodesma / Transferases; Acyltransferases; Aminoacyltransferases / transmembrane receptor protein tyrosine kinase activity / phosphorylation / transferase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, J. / Fan, F. / Gu, L. / Chai, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.7 KB | Display | ![]() |
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PDB format | ![]() | 238.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hglSC ![]() 2qkwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37330.395 Da / Num. of mol.: 4 / Mutation: D193G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Pto / Plasmid: PET-30A / Production host: ![]() ![]() #2: Protein | Mass: 9428.645 Da / Num. of mol.: 4 / Fragment: UNP residues 121-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hopAB2, avrPtoB, PSPTO_3087 / Species (production host): plasmid / Production host: ![]() ![]() References: UniProt: Q8RSY1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 7, 2008 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3HGL for AvrPtoB AND 2QKW for Pto 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.92 Å2 / Biso mean: 81.806 Å2 / Biso min: 44.12 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.297→3.38 Å / Total num. of bins used: 20
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