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- PDB-3cxb: Crystal Structure of sifa and skip -

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Basic information

Entry
Database: PDB / ID: 3cxb
TitleCrystal Structure of sifa and skip
Components
  • Pleckstrin homology domain-containing family M member 2
  • Protein sifA
KeywordsSIGNALING PROTEIN / sifa / skip / complex / Virulence / Cytoplasm / Membrane / Polymorphism
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 typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHuang, Z. / Chai, J.
CitationJournal: Cell Host Microbe / Year: 2008
Title: Structure and function of Salmonella SifA indicate that its interactions with SKIP, SseJ, and RhoA family GTPases induce endosomal tubulation
Authors: Ohlson, M.B. / Huang, Z. / Alto, N.M. / Blanc, M.P. / Dixon, J.E. / Chai, J. / Miller, S.I.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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
A: Protein sifA
B: Pleckstrin homology domain-containing family M member 2


Theoretical massNumber of molelcules
Total (without water)50,9152
Polymers50,9152
Non-polymers00
Water2,162120
1
A: Protein sifA


Theoretical massNumber of molelcules
Total (without water)38,5461
Polymers38,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pleckstrin homology domain-containing family M member 2


Theoretical massNumber of molelcules
Total (without water)12,3691
Polymers12,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.690, 110.679, 45.533
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 typhimurium (bacteria) / Gene: sifA, STM1224 / Plasmid: PET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q56061
#2: Protein Pleckstrin homology domain-containing family M member 2 / Salmonella-induced filaments A and kinesin-interacting protein / SifA and kinesin-interacting protein / SKIP


Mass: 12369.099 Da / Num. of mol.: 1 / Fragment: PH motif, UNP residues 773-884
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHM2, KIAA0842, SKIP / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IWE5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Poly acrylic acid5100, 0.05M magnesium chloride, 0.1M Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONBSRF 3W1A20.9793, 0.9792, 0.9641
DetectorDate: Oct 28, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97931
30.97921
40.96411
ReflectionResolution: 2.6→100 Å / Num. all: 14889 / Num. obs: 14191 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.032 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.472 / Num. unique all: 1492 / Rsym value: 0.356 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 694 -RANDOM
Rwork0.2582 ---
all-14191 --
obs-13497 95.3 %-
Displacement parametersBiso mean: 45.5961 Å2
Baniso -1Baniso -2Baniso -3
1-13.351 Å20 Å20 Å2
2--11.596 Å20 Å2
3----24.947 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 0 120 3335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.49
X-RAY DIFFRACTIONr_bond_refined_d0.008
LS refinement shellResolution: 2.6→2.68 Å
RfactorNum. reflection% reflection
Rfree0.4403 44 -
Rwork0.3834 --
obs-952 95.6 %

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