5WD8

Crystal structure of Legionella pneumophila effector lpg2328

• PDB DOI: https://doi.org/10.2210/pdb5WD8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Legionella pneumophila subsp. pneumophila ATCC 43290
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-07-04 Released: 2017-11-29 
• Deposition Author(s): Kozlov, G., Wong, K., Gehring, K., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.270 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Literature

Crystal structure of the Legionella effector Lem22.

Kozlov, G., Wong, K., Gehring, K.

(2018) Proteins 86: 263-267

• PubMed: 29159828 
• DOI: https://doi.org/10.1002/prot.25427
• Primary Citation of Related Structures:  
  5WD8, 5WD9


• PubMed Abstract: 
  

  Legionella pneumophila is a pathogen causing severe pneumonia in humans called Legionnaires' disease. Lem22 is a previously uncharacterized effector protein conserved in multiple Legionella strains. Here, we report the crystal structure of Lem22 from the Philadelphia strain, also known as lpg2328, at 1.40 Å resolution. The structure shows an up-and-down three-helical bundle with a significant structural similarity to a number of protein-binding domains involved in apoptosis and membrane trafficking. Sequence conservation identifies a putative functional site on the interface of helices 2 and 3. The structure is an important step toward a functional characterization of Lem22.

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Organizational Affiliation: 

Department of Biochemistry, Groupe de recherche axé sur la structure des protéines, McGill University, Montreal, QC, H3G 0B1, Canada.

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.

Macromolecule Content

• Total Structure Weight: 21.34 kDa 
• Atom Count: 1,632 
• Modelled Residue Count: 180 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lem22	A, B	91	Legionella pneumophila subsp. pneumophila ATCC 43290	Mutation(s): 0  Gene Names: lp12_2320

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.270 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.044	α = 90
b = 81.143	β = 90.81
c = 45.684	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Kozlov, G., Wong, K., Gehring, K., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references, Structure summary
• Version 1.2: 2018-04-25
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary