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- PDB-1r5e: Solution structure of the folded core of Pseudomonas syringae eff... -

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Basic information

Entry
Database: PDB / ID: 1r5e
TitleSolution structure of the folded core of Pseudomonas syringae effector protein, AvrPto
Componentsavirulence protein
KeywordsPROTEIN BINDING / three-helix bundle / omega loop
Function / homologyAvrPto / Type III secretion system, AvrPto / AvrPto superfamily / Central core of the bacterial effector protein AvrPto / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / Avirulence protein
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWulf, J. / Pascuzzi, P.E. / Martin, G.B. / Nicholson, L.K.
CitationJournal: STRUCTURE / Year: 2004
Title: The solution structure of type III effector protein AvrPto reveals conformational and dynamic features important for plant pathogenesis.
Authors: Wulf, J. / Pascuzzi, P.E. / Fahmy, A. / Martin, G.B. / Nicholson, L.K.
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: avirulence protein


Theoretical massNumber of molelcules
Total (without water)13,1171
Polymers13,1171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with favorable non-bond energy
RepresentativeModel #10closest to the average, lowest energy

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Components

#1: Protein avirulence protein


Mass: 13117.424 Da / Num. of mol.: 1 / Fragment: TrAvrPto (residues 29-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Plasmid: pFLAG-CTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: Q08242

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM TrAvrPto u-15n;10mM Na2HPO4 5mM KH2PO4 225mM NaCl pH693% H2O/7% D2O
21mM TrAvrPto u-15n,13c;10mM Na2HPO4 5mM KH2PO4 225mM NaCl pH693% H2O/7% D2O
31mM TrAvrPto u-15n,13c;10mM Na2HPO4 5mM KH2PO4 225mM NaCl pH6100% D2O
Sample conditionsIonic strength: 15mM phosphate, 245mM sodium / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1brunger, steinrefinement
NMRPipedelaglioprocessing
PIPPgarrettdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: structures are based on a total of 1898 restraints, 1584 are NOE-derived distance constraints, 206 dihedral angle restraints,108 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average, lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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