Comments on biological units for the PDB entry 1FJL

The chains A, B, D, and E describe two variants of the complex, one including nucleotide residues DA1 and DT8 of the chain D and DT1 and DA8 of the chain E; another including residues DT1 and DA8 of the chain D and DA1 and DT8 of the chain E. In the original entry, the residues, e.g, DA1 and DT1 of the chain D are described by alter codes, namely, the atoms of adenine have altercode "A" and the atoms of thymine have alter code "B". The biological unit pdb1 from the Protein Data Bank consists of both those variants superimposed. We decided to separate those two variants of the complex onto two different biological units called BEL1 and BEL2.

The chains C and F forms one-half of the third variant of the complex, which must be reconstructed using the pseudo two-fold symmetry. Analysing the structure, we understood that the reconstructed copy of the chain C must be exactly the same as the original chain C (only the values of the coordinates must differ). However, the reconstructed copy of the chain F must include only the variants with altercode "B" of the residues 1 and 8, while in the "original" copy of the chain F only the variants with altercode "A". The third biological unit BEL3 is constructed as follows. It contains two models. Both models contain the chain C, in the model 1 all atoms of the chain C have the original coordinates, in the model 2 the coordinates of the atoms are transformed according to the two-fold symmetry. The model 1 contains all atoms of the chain F except of having the altercode "B". The model 2 contains all atoms of the chain F, except of having the altercode "A"; and all coordinates of the atoms are transformed according to the two-fold symmetry.

The biological unit pdb2 from the Protein Data Bank also contains two models, but the atoms in both models are the same; so adenine and thymine are superimposed in positions 1 and 8 of the chain F.