Poly-γ-glutamate (PGA) is a major component of mucilage derived from natto, a Japanese fermented food made from soybeans, and PGAs obtained under laboratory's conditions contain numerous d-glutamyl residues. Natto foods are thus promising as a source for nutritionally safe d-amino acids present in intact and digested polymers, although there is little information on the stereochemistry of PGA isolated directly from natto. Here, we describe the development of a new process for rapid purification of PGA using alum and determined the d-glutamate content of natto PGA by chiral high-performance liquid chromatographic analysis. Further, using hexadecylpyridinium cation (HDP+), which is a compound of toothpaste, we chemically transformed natto PGA into a new thermoplastic material, called dl-PGAIC. 1H nuclear magnetic resonance and calorimetric measurements indicate that dl-PGAIC is a stoichiometric complex of natto PGA and HDP+ with glass transition points of −16.8 °C and −3.1 °C. Then, dl-PGAIC began decomposing at 210 °C, suggesting thermal stability suitable for use as a supramolecular soft plastic.