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- PDB-2fm9: Structure of Salmonella SipA residues 48-264 -

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Basic information

Entry
Database: PDB / ID: 2fm9
TitleStructure of Salmonella SipA residues 48-264
ComponentsCell invasion protein sipA
KeywordsCELL INVASION / Salmonella / type II secretion / SipA / virulence / bacterial
Function / homology
Function and homology information


actin binding / extracellular region
Similarity search - Function
SipA N-terminal domain-like / SipA N-terminal domain-like / 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 / SAD / Resolution: 2 Å
AuthorsLilic, M. / Vujanac, M. / Stebbins, C.E.
CitationJournal: Mol.Cell / Year: 2006
Title: A common structural motif in the binding of virulence factors to bacterial secretion chaperones.
Authors: Lilic, M. / Vujanac, M. / Stebbins, C.E.
History
DepositionJan 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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: Cell invasion protein sipA


Theoretical massNumber of molelcules
Total (without water)23,5821
Polymers23,5821
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.080, 71.080, 95.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

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Components

#1: Protein Cell invasion protein sipA / Effector protein sipA


Mass: 23582.234 Da / Num. of mol.: 1 / Fragment: Residues 48-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: sipA, sspA / Plasmid: pGEX-4T3 / 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.: 89 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: hanging drops formed from mixing a 1:1 volume ratio of 20mg/ml protein with an equilibration buffer consisting of 20% PEG6000, 20% glycerol, Na-citrate pH 5.6 and 0.01M adenosine-5 - ...Details: hanging drops formed from mixing a 1:1 volume ratio of 20mg/ml protein with an equilibration buffer consisting of 20% PEG6000, 20% glycerol, Na-citrate pH 5.6 and 0.01M adenosine-5 -triphosphate disodium salt (ATP) as an additive., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 19209 / Num. obs: 19209 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.031 / Χ2: 1.018
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.357 / Num. unique all: 1888 / Χ2: 1.064 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.455 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 982 5.1 %RANDOM
Rwork0.202 ---
all0.204 19166 --
obs0.204 19166 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 89 1633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221567
X-RAY DIFFRACTIONr_bond_other_d0.0010.021463
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9892113
X-RAY DIFFRACTIONr_angle_other_deg0.90733439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.77326.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.325153
X-RAY DIFFRACTIONr_chiral_restr0.1070.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02264
X-RAY DIFFRACTIONr_nbd_refined0.2280.2396
X-RAY DIFFRACTIONr_nbd_other0.1760.21307
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2794
X-RAY DIFFRACTIONr_nbtor_other0.0950.2889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.23
X-RAY DIFFRACTIONr_mcbond_it1.571.51304
X-RAY DIFFRACTIONr_mcbond_other0.3421.5404
X-RAY DIFFRACTIONr_mcangle_it1.72921608
X-RAY DIFFRACTIONr_scbond_it3.4453634
X-RAY DIFFRACTIONr_scangle_it4.6684.5505
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 79 -
Rwork0.233 1328 -
obs-1407 99.79 %
Refinement TLS params.Method: refined / Origin x: 15.339 Å / Origin y: 43.483 Å / Origin z: 17.002 Å
111213212223313233
T-0.0883 Å2-0.0356 Å20.0219 Å2--0.1998 Å2-0.04 Å2---0.1225 Å2
L3.1616 °2-0.0523 °2-1.8967 °2-1.5995 °2-1.1102 °2--4.9783 °2
S0.0722 Å °-0.2073 Å °0.0684 Å °0.2704 Å °-0.0103 Å °0.0679 Å °-0.0362 Å °-0.0723 Å °-0.0618 Å °
Refinement TLS groupSelection: ALL

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