Tpp49Aa1 from $Lysinibacillus sphaericus$ is a Toxin_10 family protein that must interact with Cry48Aa1, a 3-domain crystal protein, to produce potent mosquitocidal activity, specifically against $Culex quinquefasciatus$ mosquitoes. We use $Culex$ cell lines to demonstrate for the first time transient detrimental effects of individual toxin components and widen the known target range of the proteins. MHz serial femtosecond crystallography at a nano-focused X-ray free electron laser allowed rapid and high-quality data collection to determine the Tpp49Aa1 structure at 2.2 Å resolution from the merged X-ray diffraction data. The structure revealed the packing of Cry49Aa1 within the natural nanocrystals isolated from sporulated bacteria, as a homodimer with a large intermolecular interface. We then modelled the potential interaction between Tpp49Aa1 and Cry48Aa1. The structure sheds light on natural crystallisation and, along with cell-based assays broadens our understanding of this two-component system.