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- PDB-3hw2: Crystal structure of the SifA-SKIP(PH) complex -

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Basic information

Entry
Database: PDB / ID: 3hw2
TitleCrystal structure of the SifA-SKIP(PH) complex
Components
  • Pleckstrin homology domain-containing family M member 2
  • Protein sifA
KeywordsSIGNALING PROTEIN / sifa / protein complex / salmonella infection / late effector / Virulence / Phosphoprotein
Function / homology
Function and homology information


symbiont-mediated perturbation of host small GTPase-mediated signal transduction / symbiont-mediated perturbation of host microtubule cytoskeleton / lysosome localization / natural killer cell mediated cytotoxicity / Golgi organization / kinesin binding / regulation of protein localization / host cell cytoplasm / endosome membrane / lysosomal membrane ...symbiont-mediated perturbation of host small GTPase-mediated signal transduction / symbiont-mediated perturbation of host microtubule cytoskeleton / lysosome localization / natural killer cell mediated cytotoxicity / Golgi organization / kinesin binding / regulation of protein localization / host cell cytoplasm / endosome membrane / lysosomal membrane / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Secreted effector protein SifA helical domain / Secreted effector protein SifA fold / Secreted effector protein SifA / Salmonella typhimurium protein / Sif / Secreted effector protein SifA, C-terminal domain superfamily / Sif protein / : / RUN / RUN domain ...Secreted effector protein SifA helical domain / Secreted effector protein SifA fold / Secreted effector protein SifA / Salmonella typhimurium protein / Sif / Secreted effector protein SifA, C-terminal domain superfamily / Sif protein / : / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Rna Polymerase Sigma Factor; Chain: A / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Enolase-like; domain 1 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Secreted effector protein SifA / Pleckstrin homology domain-containing family M member 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDiacovich, L. / Dumont, A. / Lafitte, D. / Soprano, E. / Guilhon, A.-A. / Bignon, C. / Gorvel, J.-P. / Bourne, Y. / Meresse, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Interaction between the SifA virulence factor and its host target skip is essential for salmonella pathogenesis
Authors: Diacovich, L. / Dumont, A. / Lafitte, D. / Soprano, E. / Guilhon, A.-A. / Bignon, C. / Gorvel, J.-P. / Bourne, Y. / Meresse, S.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 26, 2014Group: Derived calculations
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Protein sifA
B: Pleckstrin homology domain-containing family M member 2


Theoretical massNumber of molelcules
Total (without water)50,2812
Polymers50,2812
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.799, 110.866, 44.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein sifA


Mass: 38546.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q56061
#2: Protein Pleckstrin homology domain-containing family M member 2 / SifA and kinesin-interacting protein / Salmonella-induced filaments A and kinesin-interacting protein


Mass: 11734.374 Da / Num. of mol.: 1
Fragment: Pleskrin homology (PH) domain, UNP residues 771-876
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IWE5

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 7176 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rsym value: 0.091 / Net I/σ(I): 8.9 / Num. measured all: 31607
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.41 / % possible all: 95.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CXB

3cxb


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.863 / SU B: 96.209 / SU ML: 0.694 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.76 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30925 697 9.8 %RANDOM
Rwork0.24035 ---
obs0.2473 6424 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.438 Å2
Baniso -1Baniso -2Baniso -3
1--6.27 Å20 Å20 Å2
2---4.83 Å2-0 Å2
3---11.1 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 0 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9554561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08124.494158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99315613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8081520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 74 -
Rwork0.305 442 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8029-0.92980.62827.76732.31715.06120.21160.23831.1054-0.2525-0.0294-0.1389-0.21460.3911-0.18220.04570.03490.05820.12950.0370.2054-2.054230.7886-8.0223
26.81271.354-2.92642.3589-1.10683.3025-0.00380.9923-0.1682-0.76680.24021.04140.32840.0003-0.23640.36610.0374-0.38420.301-0.02990.5627-21.935513.696-17.2564
310.406-1.32260.74039.07481.05635.33170.0985-0.5933-0.08650.6981-0.0185-1.13780.1205-0.5837-0.080.1693-0.0226-0.10050.12680.01680.151813.891413.79612.2819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 136
2X-RAY DIFFRACTION2A137 - 328
3X-RAY DIFFRACTION3B772 - 876

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