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- PDB-6cgi: Structure of Salmonella Effector SseK3 -

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Basic information

Entry
Database: PDB / ID: 6cgi
TitleStructure of Salmonella Effector SseK3
ComponentsType III secretion system effector protein
KeywordsTRANSFERASE / CELL INVASION / SseK3 / UDP-GlcNAc / glycosyltransferase / arginine-modification / bacterial effectors
Function / homologySseK/NleB family / transferase activity / nucleotide binding / metal ion binding / URIDINE-5'-DIPHOSPHATE / Type III secretion system effector arginine glycosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsChung, I.Y.W. / Cygler, M.
CitationJournal: Mol.Cell Proteomics / Year: 2019
Title: Salmonella Effectors SseK1 and SseK3 Target Death Domain Proteins in the TNF and TRAIL Signaling Pathways.
Authors: Newson, J.P.M. / Scott, N.E. / Yeuk Wah Chung, I. / Wong Fok Lung, T. / Giogha, C. / Gan, J. / Wang, N. / Strugnell, R.A. / Brown, N.F. / Cygler, M. / Pearson, J.S. / Hartland, E.L.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Mar 13, 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: Type III secretion system effector protein
B: Type III secretion system effector protein
C: Type III secretion system effector protein
D: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7178
Polymers142,1014
Non-polymers1,6174
Water5,260292
1
A: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,5251
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,5251
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,5251
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9292
Polymers35,5251
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 96.170, 90.710
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Type III secretion system effector protein


Mass: 35525.211 Da / Num. of mol.: 4 / Fragment: residues 25-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: sseK3, SL1344_1928 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3NMP8
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.5M NaCl, 0.1M Tris pH8.5, 18% PEG 3350 5%MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9801 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→48.36 Å / Num. obs: 56770 / % possible obs: 99.8 % / Redundancy: 4 % / Rrim(I) all: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.35 Å / Num. unique obs: 16899 / Rrim(I) all: 0.595

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.36 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.2502 2835 5 %
Rwork0.2172 --
obs0.2188 56699 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9649 100 0 292 10041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049979
X-RAY DIFFRACTIONf_angle_d0.81313498
X-RAY DIFFRACTIONf_dihedral_angle_d9.1375908
X-RAY DIFFRACTIONf_chiral_restr0.0521434
X-RAY DIFFRACTIONf_plane_restr0.0031757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33980.35581430.28642708X-RAY DIFFRACTION100
2.3398-2.38230.36711400.27882659X-RAY DIFFRACTION100
2.3823-2.42810.30151410.27062669X-RAY DIFFRACTION100
2.4281-2.47770.29131420.2652709X-RAY DIFFRACTION100
2.4777-2.53160.32361420.26632683X-RAY DIFFRACTION100
2.5316-2.59040.30171410.26122673X-RAY DIFFRACTION100
2.5904-2.65520.34371410.26132682X-RAY DIFFRACTION100
2.6552-2.7270.29861400.26242661X-RAY DIFFRACTION100
2.727-2.80720.3031420.24942687X-RAY DIFFRACTION100
2.8072-2.89780.28721410.24692687X-RAY DIFFRACTION100
2.8978-3.00140.30191420.23952696X-RAY DIFFRACTION100
3.0014-3.12160.25581430.23412709X-RAY DIFFRACTION100
3.1216-3.26360.29271410.23222674X-RAY DIFFRACTION100
3.2636-3.43560.2691400.21862690X-RAY DIFFRACTION100
3.4356-3.65080.20461410.19622688X-RAY DIFFRACTION100
3.6508-3.93260.19071430.182718X-RAY DIFFRACTION100
3.9326-4.32810.18871420.17062686X-RAY DIFFRACTION100
4.3281-4.95380.18451420.16912707X-RAY DIFFRACTION100
4.9538-6.23920.23671430.21312721X-RAY DIFFRACTION100
6.2392-48.37050.21351450.19072757X-RAY DIFFRACTION99

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