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- PDB-3hgl: crystal of AvrPtoB 121-205 -

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Basic information

Entry
Database: PDB / ID: 3hgl
Titlecrystal of AvrPtoB 121-205
ComponentsEffector protein hopAB2
KeywordsLIGASE / five helices / Hypersensitive response elicitation / 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 defense-related programmed cell death / Transferases; Acyltransferases; Aminoacyltransferases / transferase activity / extracellular region
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 / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Effector protein HopAB2
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDong, J. / Xiao, F. / Fan, F. / Gu, L. / Cang, H. / Martin, G.B. / 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Effector protein hopAB2


Theoretical massNumber of molelcules
Total (without water)9,6161
Polymers9,6161
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.220, 77.220, 46.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Effector protein hopAB2 / AvrPtoB / Avirulence protein avrPtoB / E3 ubiquitin-protein ligase


Mass: 9616.225 Da / Num. of mol.: 1 / 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 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RSY1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% (v/v) Tacsimate, pH 7.0, 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: 0.9789, 0.9794, 0.9764
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 7, 2008
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97941
30.97641
ReflectionResolution: 1.9→99 Å / Num. all: 12921 / Num. obs: 12921 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.33 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 624 5 %RANDOM
Rwork0.235 ---
all-12921 --
obs-12921 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 0 61 666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.119
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.28 48 -
Rwork0.28 1004 -
obs--99 %

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