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- PDB-1r9k: Representative solution structure of the catalytic domain of SopE2 -

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Basic information

Entry
Database: PDB / ID: 1r9k
TitleRepresentative solution structure of the catalytic domain of SopE2
ComponentsTypeIII-secreted protein effector: invasion-associated protein
KeywordsCELL INVASION / Salmonella / invasion / type III / GEF / SopE
Function / homology
Function and homology information


GTPase activator activity / guanyl-nucleotide exchange factor activity / actin cytoskeleton organization / extracellular region
Similarity search - Function
Guanine nucleotide exchange factor SopE, N-terminal domain / Salmonella type III secretion SopE effector N-terminus / SopE-like, GEF domain / Guanine nucleotide exchange factor SopE / Guanine nucleotide exchange factor SopE, GEF domain / SopE-like, GEF domain superfamily / SopE GEF domain / SopE-like GEF fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Guanine nucleotide exchange factor sopE2 / Guanine nucleotide exchange factor sopE2
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWilliams, C. / Galyov, E.E. / Bagby, S.
Citation
Journal: Biochemistry / Year: 2004
Title: Solution Structure, Backbone Dynamics, and Interaction with Cdc42 of Salmonella Guanine Nucleotide Exchange Factor SopE2(,).
Authors: Williams, C. / Galyov, E.E. / Bagby, S.
#1: Journal: To be Published / Year: 2003
Title: Biochemical and structural analysis of Salmonella and Burkholderia virulence proteins
Authors: Williams, C.
#2: Journal: J.BIOMOL.NMR / Year: 2003
Title: Assignment of the 1H,13C and 15N resonances of the catalytic domain of guanine nucelotide exchange factor SopE2 from Salmonella dublin
Authors: Williams, C. / Galyov, E.E. / Bagby, S.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 21, 2012Group: Other
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TypeIII-secreted protein effector: invasion-associated protein


Theoretical massNumber of molelcules
Total (without water)18,5851
Polymers18,5851
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)1 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein TypeIII-secreted protein effector: invasion-associated protein


Mass: 18585.338 Da / Num. of mol.: 1 / Fragment: SopE2 GEF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: sopE2 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KIZ2, UniProt: Q7CQD4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
2222D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
353HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SopE2 U-15N,13C; 20mM HEPES buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21mM SopE2 unlabelled; 20mM tris buffer; 99.6% D2O99.6% D2O
31mM SopE2 U-15N; 20mM HEPES buffer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
107ambient 298 K
207ambient 298 K
307ambient 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio et alprocessing
Sparky3.1Goddard & knellerdata analysis
XPLOR-NIH2.06Schwieters et alstructure solution
XPLOR-NIH2.06Schwieters et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: he structures are based on a total of 3065 restraints, 2682 are NOE-derived distance constraints, 249 dihedral angle restraints,134 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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