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Mms6 is a protein that plays crucial role in the biomineralization and formation of magnetosomes in magnetotactic bacteria Magnetospirillum magneticum (strain AMB-1). We developed a fusion protein of C-term part of Mms6 and Barstar (natural inhibitor of ribonuclease Barnase), namely, Bs-C-Mms6. This protein successfully stabilized uncoated monocrystalline Fe3O4 magnetite nanoparticles in buffered solutions. Here, we present data regarding the synthesis and characterization of magnetite nanoparticles stabilized with Bs-C-Mms6. For further interpretation of the data presented in this article, please see the research article ‘Self-assembling nanoparticles biofunctionalized with magnetite-binding protein for the targeted delivery to HER2/neu overexpressing cancer cells’ (Shipunova et al., 2018) [1].