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- PDB-1jyo: Structure of the Salmonella Virulence Effector SptP in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 1jyo
TitleStructure of the Salmonella Virulence Effector SptP in Complex with its Secretion Chaperone SicP
Components
  • SicP
  • protein tyrosine phosphatase SptP
KeywordsCHAPERONE / Salmonella / bacterial pathogenesis / infectious disease / virulence factor / type III secretion / unfolded / protein folding / SptP / SicP
Function / homology
Function and homology information


: / protein secretion by the type III secretion system / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / GTPase activator activity / host cell cytoplasm / extracellular space / cytoplasm
Similarity search - Function
non globular Virulence effector SptP fold / non globular Virulence effector SptP domain / Chaperone protein SicP / Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Bacterial Rho GTPase-activating protein (GAP) domain profile. / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) ...non globular Virulence effector SptP fold / non globular Virulence effector SptP domain / Chaperone protein SicP / Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Bacterial Rho GTPase-activating protein (GAP) domain profile. / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Type III secreted modular tyrosine phosphatase, SptP/YopH / Yope Regulator; Chain: A, / : / Globular protein, non-globular alpha/beta subunit / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chaperone protein SicP / Chaperone protein SicP / Secreted effector protein SptP
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsStebbins, C.E. / Galan, J.E.
CitationJournal: Nature / Year: 2001
Title: Maintenance of an unfolded polypeptide by a cognate chaperone in bacterial type III secretion.
Authors: Stebbins, C.E. / Galan, J.E.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE An appropriate sequence database match was not available at the time of processing. The ...SEQUENCE An appropriate sequence database match was not available at the time of processing. The authors state that the gene that was originally reported to Genbank accession code 3283218 was short by 15 residues. There are two potential start sites for trasncription of this gene, and biochemical work convinced them that the protein requires the additional amino acids at the N-terminus to function optimally, and the other sequence is likely a truncation.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SicP
B: SicP
C: SicP
D: SicP
E: protein tyrosine phosphatase SptP
F: protein tyrosine phosphatase SptP


Theoretical massNumber of molelcules
Total (without water)81,7636
Polymers81,7636
Non-polymers00
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17790 Å2
ΔGint-141 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.489, 49.582, 138.142
Angle α, β, γ (deg.)90.00, 121.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SicP


Mass: 14457.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O85300, UniProt: P0CL16*PLUS
#2: Protein protein tyrosine phosphatase SptP


Mass: 11966.853 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P74873
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M sodium chloride, 5-10% polyethylene glycol molecular weight 6000 (PEG6000), supplemented with 2mM DTT and 15% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mlprotein1drop
22 M1reservoirNaCl
35-10 %PEG60001reservoir
42 mMdithiothreitol1reservoir
515 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.0051 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0051 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 75880 / Num. obs: 75880 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.045 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.243 / % possible all: 74.3
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 452315 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 74.3 % / Rmerge(I) obs: 0.243

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 3800 random
Rwork0.224 --
all0.226 75880 -
obs0.226 75880 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5706 0 0 629 6335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. reflection obs: 70014 / σ(F): 0 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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