We calculate the partial molar volume (PMV) of 20 amino acids in aqueous solution at infinite dilution by using the Kirkwood-Buff equation and the three-dimensional reference interaction site model (3D-RISM) integral equation theory for molecular liquids. As compared to the conventional, one-dimensional (1D-RISM) approach, the results exhibit drastic improvement for the quantitative agreement with experiments. The deviation from the experimental data seen for the relatively large amino acids is discussed in terms of the "ideal fluctuation volume" introduced in the previous study based on the 1D-RISM. Robustness of the new approach is further demonstrated by applying it to the PMV of polyglutamic acids in aqueous solution. The method provides reasonable account for the PMV increase with the chain length, both in alpha -helical and extended structures, whereas the 1D-RISM approach gives an unnatural decrease of the PMV for the alpha helix with a complete turn of the backbone.