Photoemission ( PE) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy were applied to characterize electronic properties of the regular two-dimensional bacterial surface protein layer ( S layer) of Bacillus sphaericus NCTC 9602, which is widely used as a protein template for the bottom-up fabrication of advanced metallic and hybrid nanostructures. PE and NEXAFS at the C 1s, O 1s, and N 1s core levels show similar chemical states for each oxygen atom and also for each nitrogen atom, while carbon atoms exhibit a range of chemical environments in different functional groups of the amino acids. A series of characteristic NEXAFS peaks were assigned to particular molecular orbitals of the amino acids by applying a phenomenological building block model. It was found that the p clouds of aromatic rings make the main contribution to both the lowest unoccupied and highest occupied molecular orbitals. The two-dimensional protein crystal shows a semiconductor-like behaviour with a gap value of similar to 3.0 eV and the Fermi energy close to the bottom of the LUMO.