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- PDB-6eyr: Crystal structure of the salmonella effector SseK3 -

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Basic information

Entry
Database: PDB / ID: 6eyr
TitleCrystal structure of the salmonella effector SseK3
ComponentsType III secretion system effector proteinType three secretion system
KeywordsTOXIN / Glycosyltransferase / GlcNAc / effector protein
Function / homologytransferase activity / Type III secretion system effector arginine glycosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEsposito, D. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the glycosyltransferase activity of theSalmonellaeffector SseK3.
Authors: Esposito, D. / Gunster, R.A. / Martino, L. / El Omari, K. / Wagner, A. / Thurston, T.L.M. / Rittinger, K.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 1, 2024Group: 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: Type III secretion system effector protein
B: Type III secretion system effector protein


Theoretical massNumber of molelcules
Total (without water)73,4262
Polymers73,4262
Non-polymers00
Water5,729318
1
A: Type III secretion system effector protein


Theoretical massNumber of molelcules
Total (without water)36,7131
Polymers36,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III secretion system effector protein


Theoretical massNumber of molelcules
Total (without water)36,7131
Polymers36,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.612, 86.047, 95.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type III secretion system effector protein / Type three secretion system


Mass: 36712.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SL1344 / Gene: sseK3, SL1344_1928 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0H3NMP8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 0.2 M NaCl and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9764 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.2→58.24 Å / Num. obs: 31246 / % possible obs: 99.42 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1509 / Rpim(I) all: 0.05927 / Rrim(I) all: 0.1624 / Net I/σ(I): 7.79
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.6784 / Rpim(I) all: 0.2654 / Rrim(I) all: 0.7296

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S-SAD structure

Resolution: 2.2→58.24 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.2582 1543 4.94 %
Rwork0.2171 --
obs0.2191 31209 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→58.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 0 318 5179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034980
X-RAY DIFFRACTIONf_angle_d0.676724
X-RAY DIFFRACTIONf_dihedral_angle_d6.0253585
X-RAY DIFFRACTIONf_chiral_restr0.048714
X-RAY DIFFRACTIONf_plane_restr0.004883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1995-2.27050.3051130.27552674X-RAY DIFFRACTION99
2.2705-2.35170.33011320.26532659X-RAY DIFFRACTION100
2.3517-2.44580.33961430.26282659X-RAY DIFFRACTION100
2.4458-2.55720.31681340.25392694X-RAY DIFFRACTION100
2.5572-2.6920.28471380.2552694X-RAY DIFFRACTION100
2.692-2.86060.28221500.23852653X-RAY DIFFRACTION100
2.8606-3.08150.23181380.23152722X-RAY DIFFRACTION100
3.0815-3.39160.2851420.21312590X-RAY DIFFRACTION96
3.3916-3.88230.23741640.19182691X-RAY DIFFRACTION99
3.8823-4.8910.19991390.17152744X-RAY DIFFRACTION100
4.891-63.86840.23761500.19932886X-RAY DIFFRACTION100

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