8PX1 | pdb_00008px1

Structure of salmonella effector SseK3, solved at wavelength 2.75 A

• PDB DOI: https://doi.org/10.2210/pdb8PX1/pdb

• Classification: TOXIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-22 Released: 2023-10-25 
• Deposition Author(s): El Omari, K., Duman, R., Mykhaylyk, V., Orr, C.M., Esposito, D., Rittinger, K., Wagner, A.
• Funding Organization(s): Diamond Light Source

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.293 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Literature

Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.

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.

(2023) Commun Chem 6: 219-219

• PubMed: 37828292 
• DOI: https://doi.org/10.1038/s42004-023-01014-0
• Primary Citation Related Structures: 
  8PWN, 8PX0, 8PX1, 8PX4, 8PX5, 8PX7, 8PX9, 8PXC, 8PXG, 8PXH, 8PXJ, 8PXK, 8PXL, 8PYV, 8PYZ, 8PZ4, 8PZ5


• PubMed Abstract: 
  

  Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.

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Organizational Affiliation: 
• Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
Department of Biochemistry, University of Oxford, Oxford, UK.
Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy.
Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK.
Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan.
Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.
School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil.
The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK.
Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK. [e-mail].
Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.21 kDa 
• Atom Count: 9,913 
• Modeled Residue Count: 1,224 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-LEE encoded effector protein NleB	A, B, C, D	320	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: sseK
UniProt
Find proteins for A0A3V0J4I0 (Salmonella typhimurium) Explore A0A3V0J4I0  Go to UniProtKB:  A0A3V0J4I0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.293 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.08	α = 90
b = 75.02	β = 109.52
c = 101.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): El Omari, K., Duman, R., Mykhaylyk, V., Orr, C.M., Esposito, D., Rittinger, K., Wagner, A.

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Funding Organization	Location	Grant Number
Diamond Light Source	United Kingdom	--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection
• Version 1.2: 2024-11-06
  Changes: Structure summary