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- PDB-1q5z: Crystal Structure of the C-terminal Actin Binding Domain of Salmo... -

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Basic information

Entry
Database: PDB / ID: 1q5z
TitleCrystal Structure of the C-terminal Actin Binding Domain of Salmonella Invasion Protein A (SipA)
ComponentsSipA
KeywordsCELL INVASION
Function / homology
Function and homology information


actin binding / extracellular region
Similarity search - Function
Invasion protein A fold / Salmonella invasion protein A, C-terminal actin-binding domain / Salmonella invasion protein A, C-terminal actin-binding domain superfamily / : / Salmonella Invasion protein A, C-terminal actin binding domain / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell invasion protein SipA / Cell invasion protein SipA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsStebbins, C.E. / Lilic, M. / Galkin, V.E. / Orlova, A. / VanLoock, M.S. / Egelman, E.H.
CitationJournal: Science / Year: 2003
Title: Salmonella SipA polymerizes actin by stapling filaments with nonglobular protein arms.
Authors: Lilic, M. / Galkin, V.E. / Orlova, A. / VanLoock, M.S. / Egelman, E.H. / Stebbins, C.E.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: SipA


Theoretical massNumber of molelcules
Total (without water)19,4551
Polymers19,4551
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.900, 79.900, 57.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein SipA / Salmonella invasion protein A / SIPA


Mass: 19454.939 Da / Num. of mol.: 1 / Fragment: C-terminal actin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: SipA / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56027, UniProt: P0CL52*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 1.5% methyl-pentanediol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
210 mMTris1droppH8.0
3100 mM1dropNaCl
42 mMdithiothreitol1drop
52 Mammonium sulfate1reservoir
61.5 %MPD1reservoirpH7.5
72 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9792,0.9794,0.9716
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2002 / Details: X9A
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.97161
ReflectionResolution: 1.8→30 Å / Num. all: 17843 / Num. obs: 17011 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 17843 / % possible obs: 99.9 % / Num. measured all: 476002 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.222 836 random
Rwork0.194 --
all0.194 17788 -
obs0.194 17011 -
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 220 1356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26569
X-RAY DIFFRACTIONc_bond_d0.007649
LS refinement shellResolution: 1.8→1.84 Å /
RfactorNum. reflection
Rfree0.26 41
Rwork0.22 -
obs-944
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.26
LS refinement shell
*PLUS
Highest resolution: 1.8 Å

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