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- PDB-7ym7: Crystal structure of the Salmonella effector SseK1 F187A mutant -

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Basic information

Entry
Database: PDB / ID: 7ym7
TitleCrystal structure of the Salmonella effector SseK1 F187A mutant
ComponentsType III secretion system effector arginine glycosyltransferase SseK1
KeywordsTOXIN / salmonella / effector / arginine glycosylation
Function / homologytransferase activity / Type III secretion system effector arginine glycosyltransferase SseK1
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, U.J. / Park, J.B. / Yoo, Y. / Cho, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Sci Rep / Year: 2022
Title: Catalytic DxD motif caged in Asx-turn and Met-aromatic interaction attenuates the pathogenic glycosylation of SseK2/NleB2 effectors.
Authors: Koh, E. / Kim, U. / Cho, H.S.
History
DepositionJul 27, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 2, 2023ID: 6IXK
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III secretion system effector arginine glycosyltransferase SseK1
B: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)70,2152
Polymers70,2152
Non-polymers00
Water724
1
A: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)35,1081
Polymers35,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)35,1081
Polymers35,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.380, 47.760, 81.780
Angle α, β, γ (deg.)90.000, 97.930, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Type III secretion system effector arginine glycosyltransferase SseK1


Mass: 35107.641 Da / Num. of mol.: 2 / Mutation: F187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: G3V45_004211, G4O83_004375, G4X61_004300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A735ZBM9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate 0.1 M MES:NaOH pH 6.5 30% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.09 Å / Num. obs: 34504 / % possible obs: 98.73 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06397 / Rpim(I) all: 0.03048 / Rrim(I) all: 0.07112 / Net I/σ(I): 15.03
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 3381 / CC1/2: 0.819 / CC star: 0.949 / Rpim(I) all: 0.577 / Rrim(I) all: 0.07112 / % possible all: 97.77

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.09 Å / SU ML: 0.3928 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 1709 4.96 %
Rwork0.2417 32748 -
obs0.2429 34457 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 0 4 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01254900
X-RAY DIFFRACTIONf_angle_d1.60166598
X-RAY DIFFRACTIONf_chiral_restr0.0878695
X-RAY DIFFRACTIONf_plane_restr0.0064865
X-RAY DIFFRACTIONf_dihedral_angle_d15.89531836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.41731220.36932678X-RAY DIFFRACTION97.87
2.26-2.340.38441490.33982707X-RAY DIFFRACTION98.18
2.34-2.420.36861310.33122699X-RAY DIFFRACTION98.5
2.42-2.520.36091350.30972702X-RAY DIFFRACTION98.75
2.52-2.630.32011450.30612712X-RAY DIFFRACTION98.59
2.63-2.770.32071590.31392680X-RAY DIFFRACTION98.51
2.77-2.950.2941600.27842708X-RAY DIFFRACTION98.93
2.95-3.170.28841590.2632713X-RAY DIFFRACTION98.83
3.17-3.490.30741380.26062729X-RAY DIFFRACTION99.2
3.49-40.26251450.22922743X-RAY DIFFRACTION98.67
4-5.030.21281350.19382790X-RAY DIFFRACTION99.39
5.04-46.090.20841310.20482887X-RAY DIFFRACTION99.44

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