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- PDB-8px1: Structure of salmonella effector SseK3, solved at wavelength 2.75 A -

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Basic information

Entry
Database: PDB / ID: 8px1
TitleStructure of salmonella effector SseK3, solved at wavelength 2.75 A
ComponentsNon-LEE encoded effector protein NleB
KeywordsTOXIN / Salmonella -secreted effector SseK3
Function / homologytransferase activity / Type III secretion system effector arginine glycosyltransferase
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Esposito, D. / Rittinger, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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

Downloads & links

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Assembly

Deposited unit
A: Non-LEE encoded effector protein NleB
B: Non-LEE encoded effector protein NleB
C: Non-LEE encoded effector protein NleB
D: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)145,2054
Polymers145,2054
Non-polymers00
Water2,828157
1
A: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)36,3011
Polymers36,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)36,3011
Polymers36,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)36,3011
Polymers36,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)36,3011
Polymers36,3011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.080, 75.020, 101.890
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Non-LEE encoded effector protein NleB


Mass: 36301.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sseK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3V0J4I0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.73 %
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: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.1→49.93 Å / Num. obs: 62053 / % possible obs: 77.31 % / Redundancy: 23 % / Biso Wilson estimate: 36.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1655 / Rpim(I) all: 0.03484 / Rrim(I) all: 0.1693 / Net I/σ(I): 13.34
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 1.796 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4943 / CC1/2: 0.703 / Rpim(I) all: 0.3808

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.313 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29317 2978 4.8 %RANDOM
Rwork0.25187 ---
obs0.25387 59075 77.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.995 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å2-0.32 Å2
2---3.71 Å2-0 Å2
3---5.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 0 157 9913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179096
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.63813476
X-RAY DIFFRACTIONr_angle_other_deg1.3721.57521212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38323.556540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.242151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9441544
X-RAY DIFFRACTIONr_chiral_restr0.0590.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022036
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7434.3484892
X-RAY DIFFRACTIONr_mcbond_other3.744.3484891
X-RAY DIFFRACTIONr_mcangle_it5.6126.516108
X-RAY DIFFRACTIONr_mcangle_other5.6126.5116109
X-RAY DIFFRACTIONr_scbond_it4.5094.8845088
X-RAY DIFFRACTIONr_scbond_other4.5094.8855089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0997.1137369
X-RAY DIFFRACTIONr_long_range_B_refined10.62940657
X-RAY DIFFRACTIONr_long_range_B_other10.6340650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A102630.01
12B102630.01
21A102450.02
22C102450.02
31A102610.01
32D102610.01
41B102490.01
42C102490.01
51B102650.01
52D102650.01
61C102580.01
62D102580.01
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 177 -
Rwork0.453 3481 -
obs--62.24 %

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