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- PDB-6dus: Structure of Salmonella Effector SseK3 E258Q mutant -

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Basic information

Entry
Database: PDB / ID: 6dus
TitleStructure of Salmonella Effector SseK3 E258Q mutant
ComponentsType III secretion system effector proteinType three secretion system
KeywordsTRANSFERASE / glycosyltransferase / death receptor signaling
Function / homologytransferase activity / URIDINE-5'-DIPHOSPHATE / Type III secretion system effector arginine glycosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChung, I.Y.W. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
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
DepositionJun 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 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 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09012
Polymers70,3102
Non-polymers1,78010
Water3,351186
1
A: Type III secretion system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2858
Polymers35,1551
Non-polymers1,1307
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)35,8054
Polymers35,1551
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.490, 107.120, 74.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 35154.852 Da / Num. of mol.: 2 / Mutation: E258Q
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.5M NaCl, 0.1M Tris pH8.5, 12% PEG 3350 5%MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→74.74 Å / Num. obs: 24555 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.99 / Net I/σ(I): 18.75
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 12225 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→74.73 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.2246 1196 4.89 %
Rwork0.1777 --
obs0.18 24471 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→74.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 34 186 5155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035080
X-RAY DIFFRACTIONf_angle_d0.6856882
X-RAY DIFFRACTIONf_dihedral_angle_d7.2512980
X-RAY DIFFRACTIONf_chiral_restr0.047740
X-RAY DIFFRACTIONf_plane_restr0.005883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70420.28651360.21982542X-RAY DIFFRACTION100
2.7042-2.82720.25911350.20772528X-RAY DIFFRACTION100
2.8272-2.97630.26811030.20782571X-RAY DIFFRACTION100
2.9763-3.16280.241490.19392525X-RAY DIFFRACTION100
3.1628-3.4070.21821400.17932562X-RAY DIFFRACTION100
3.407-3.74980.23121310.17112584X-RAY DIFFRACTION100
3.7498-4.29240.18491220.15332590X-RAY DIFFRACTION100
4.2924-5.40770.19511340.15222635X-RAY DIFFRACTION100
5.4077-74.76080.23511460.18722738X-RAY DIFFRACTION100

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