8POS

Crystal structure of wolbachia leucyl-tRNA synthetase editing domain bound to cmpd9-AMP adduct

• PDB DOI: https://doi.org/10.2210/pdb8POS/pdb

• Classification: LIGASE
• Organism(s): Wolbachia endosymbiont strain TRS of Brugia malayi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-05 Released: 2024-06-12 
• Deposition Author(s): Palencia, A., Hoffmann, G.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), iNEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.253 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Targeting A Microbiota Wolbachian Aminoacyl-tRNA Synthetase To Block Its Pathogenic Host

Palencia, A., Hoffmann, G., Lukarska, M., Clare, R., Ward, S., Taylor, M.A., Ringkjobing Jensen, M.

(2024) Science Advances 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.65 kDa 
• Atom Count: 2,814 
• Modelled Residue Count: 333 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine--tRNA ligase	A, B	179	Wolbachia endosymbiont strain TRS of Brugia malayi	Mutation(s): 0  Gene Names: leuS, Wbm0605 EC: 6.1.1.4
UniProt
Find proteins for Q5GS31 (Wolbachia sp. subsp. Brugia malayi (strain TRS)) Explore Q5GS31  Go to UniProtKB:  Q5GS31

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7RZ (Subject of Investigation/LOI)	C [auth A], E [auth B]	[(1R,3'S,5S,6R,8R)-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3H-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate C29 H35 B Br N7 O9 P OOVYGSSPEYCEFD-LIBJEQSZSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.253 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.147	α = 90
b = 52.147	β = 90
c = 273.558	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Palencia, A., Hoffmann, G.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-AMRB-0003-01 AntibiOxaborole
Agence Nationale de la Recherche (ANR)	France	ANR JCJC RC18114CC NovoTargetParasite
iNEXT	European Union	653706

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release