Temperature only really makes sense for macroscopic systems. A lone atom has an energy, but not a temperature. That's because temperature is defined as a derivative:
$$\frac{1}{T} = \frac{\mathrm{d}S}{\mathrm{d}E}$$
The derivative doesn't really make sense on a microscopic scale because states are quantized. On a macroscopic scale, we smooth over the states, and treat the system as having a "density of states", such that the number of states varies smoothly with energy. Absolute zero is not possible to reach because you can't reasonably treat the system as continuous for very small changes in energy, and the mathematics are invalid.