view article

Figure 7
Example of a PDB header with links and modifications. REFMAC5 is able to read the header of a PDB coordinate file and to process the information needed for restraint generation. In this example lines 1–2 give column numbers which define the format of the various links and modifications. Note that links and modifications must strictly obey the format shown here. Lines 3–4 are examples of `S' links. Line 5 is an example of metal–ligand link in which the target value is defined in the PDB file. Lines 6–11 list the links required to refine the structure given in Fig. 8[link]. The dictionary file that describes the `BEN-MAF' and `GLU-MAF' links as well as the monomers is given as supplementary material . A more detailed description of the lines in this example is as follows. Lines 1–2, column numbers in the file; line 3, `S' link between alternative conformations. The SG atom of Cys121 belonging to chain A (alternative conformation A) is bound to the SG atom of Cys222 of the same chain (alternative conformation B). Line 4, `S' link between symmetry-related Cys residues (Cys298 of chain A). The `SSBOND' record has the same meaning as in the PDB convention. `4555' is a symmetry indicator. When defining a link between symmetry-related residues, the symmetry operator does not have to be the correct one relating the two residues. It is simply a signal for the program to find the actual symmetry for the link. Line 5, `HIS-ZN' link between the NE2 atom of His71 belonging to chain A and the Zn5 atom in chain R. The target distance is 2.055 Å. Line 6, `BEN-MAF' link between the B conformation of the monomer BEN1 (atom C6, chain B) and the B conformation of the monomer MAF2 (O1, S). The `BEN-MAF' link description is not amongst those defined in the dictionary. It needs to be defined by the user. This is best performed using an existing link as a template. Line 7, `GLU-MAF' link between the A conformation of Glu320 (OE2, A) and A conformation of MAF2 (C1, S). Similarly to the `BEN-MAF' link, the `GLU-MAF' link needs to be defined by the user. Lines 8–9, `RENAME' modifications. These explicitly state that residues MAN3 and MAN4 in chain S are β-D-mannose monomers. Lines 10–11, `BETA1-4' links between MAF2 and MAN3 in chain S and between MAN2 and MAN4 in the same chain.

Journal logoBIOLOGICAL
ISSN: 1399-0047
Follow Acta Cryst. D
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds