Herein, we investigate the use of proteins with tunable DNA modification distributions to modulate nanoparticle superlattice structure. Using beta-galactosidase (beta gal) as a model system, we have employed the orthogonal chemical reactivities of surface amines and thiols to synthesize protein DNA conjugates with 36 evenly distributed or 8 specifically positioned oligonucleotides. When these are assembled into crystalline super lattices with gold nanoparticles, we find that the distribution of DNA modifications modulates the favored structure: beta gal with uniformly distributed DNA bonding elements results in body-centered cubic crystals, whereas DNA functionalization of cysteines results in AB(2) packing. We probe the role of protein oligonucleotide number and conjugate size on this observation, which revealed the importance of oligonucleotide distribution in this observed assembly behavior. These results indicate that proteins with defined DNA modification patterns are powerful tools for controlling nanoparticle superlattices architecture, and establish the importance of oligonucleotide distribution in the assembly behavior of protein-DNA conjugates.