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- PDB-7ym5: Crystal structure of the Salmonella effector SseK1 -

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Basic information

Entry
Database: PDB / ID: 7ym5
TitleCrystal structure of the Salmonella effector SseK1
ComponentsType III secretion system effector arginine glycosyltransferase SseK1
KeywordsTOXIN / salmonella / effector / arginine glycosylation
Function / homologytransferase activity / : / URIDINE-5'-DIPHOSPHATE / Type III secretion system effector arginine glycosyltransferase SseK1
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.45 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: 6AGU
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 / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8793
Polymers35,4201
Non-polymers4592
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-13 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.995, 115.995, 101.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

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


Mass: 35420.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: G9F52_004249 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A741VJQ1
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris propane-HCl pH 7.0 1.0M ammonium citrate tribasic

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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 16M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.45→44.98 Å / Num. obs: 5663 / % possible obs: 99.7 % / Redundancy: 28 % / Biso Wilson estimate: 112.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1506 / Rpim(I) all: 0.02896 / Rrim(I) all: 0.1534 / Net I/σ(I): 23.08
Reflection shellResolution: 3.45→3.573 Å / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 553 / CC1/2: 0.963 / CC star: 0.991 / Rpim(I) all: 0.2205 / Rrim(I) all: 1.232

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
iMOSFLMdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.45→44.98 Å / SU ML: 0.6022 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.3045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2898 567 10 %
Rwork0.2831 9018 -
obs0.2838 5653 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.41 Å2
Refinement stepCycle: LAST / Resolution: 3.45→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 26 1 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01152548
X-RAY DIFFRACTIONf_angle_d1.70563439
X-RAY DIFFRACTIONf_chiral_restr0.116360
X-RAY DIFFRACTIONf_plane_restr0.0064445
X-RAY DIFFRACTIONf_dihedral_angle_d13.1883937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.630.39291440.37871302X-RAY DIFFRACTION99.86
3.63-3.860.41381430.33561284X-RAY DIFFRACTION99.86
3.86-4.160.32481450.29241284X-RAY DIFFRACTION99.86
4.16-4.570.29461440.27321271X-RAY DIFFRACTION99.58
4.58-5.230.24631430.28891284X-RAY DIFFRACTION99.86
5.24-6.590.32471420.32961292X-RAY DIFFRACTION100

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