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- PDB-1g4w: CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPA... -

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Basic information

Entry
Database: PDB / ID: 1g4w
TitleCRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP
ComponentsPROTEIN TYROSINE PHOSPHATASE SPTP
KeywordsSIGNALING PROTEIN / virulence factor / tyrosine phosphatase / GTPase activating protein / 4-helix bundle / disorder
Function / homology
Function and homology information


protein-tyrosine-phosphatase / GTPase activator activity / protein tyrosine phosphatase activity / host cell cytoplasm / extracellular space
Similarity search - Function
Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Virulence factor YopE uncharacterised domain / Bacterial Rho GTPase-activating protein (GAP) domain profile. / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / : ...Secreted effector protein SptP, N-terminal domain / SicP binding / Secreted effector protein SptP, N-terminal domain superfamily / Virulence factor YopE uncharacterised domain / Bacterial Rho GTPase-activating protein (GAP) domain profile. / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Type III secreted modular tyrosine phosphatase, SptP/YopH / : / Globular protein, non-globular alpha/beta subunit / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Secreted effector protein SptP
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsStebbins, C.E. / Galan, J.E.
CitationJournal: Mol.Cell / Year: 2000
Title: Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.
Authors: Stebbins, C.E. / Galan, J.E.
History
DepositionOct 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: PROTEIN TYROSINE PHOSPHATASE SPTP


Theoretical massNumber of molelcules
Total (without water)42,1281
Polymers42,1281
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.966, 153.611, 175.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROTEIN TYROSINE PHOSPHATASE SPTP


Mass: 42127.801 Da / Num. of mol.: 1 / Fragment: SPTP RESIDUES 161-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: SPTP / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P74873
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.5M sodium formate, 2mM DTT, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 mg/mlprotein1drop
23.5 Msodium formate1reservoir
32 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 21, 1999 / Details: Yale mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24740 / Num. obs: 23440 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.93 / % possible all: 94.9
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 114569

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.314 21650 7% random with CNS
Rwork0.26 --
all0.26 24740 -
obs0.26 23440 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 0 154 2810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.2→2.23 Å /
RfactorNum. reflection
Rfree0.392 46
Rwork0.381 -
obs-645
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / Rfactor Rwork: 0.381

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