Dear all,
I submit the strange situation we are encountering to the collective
intelligence of this platform.
The current PDB policy is that a polymeric entity should be fully
modeled within the asymmetric unit. It can't be partially modeled and
built by symmetry in the unit cell.
We have several new structures of proteins in complex with synthetic
helical structures that accept a crystallographic C2 axis. In the
correct space group, the asymmetric unit contains one protein and half
of the synthetic helical structure. However, for the purpose of
deposition, we have been asked to remove this symmetry element, use a
lower symmetry space group, and model a twice-as-large asymmetric unit
that contains the entire synthetic helix and two proteins.
In another structure under refinement, with have a D-backbone covalently
linked to its L-enantiomer that crystalized in P-1 with a center of
symmetry in the middle of the linker. I expect that we will have to
deposit this structure in P1 to abide with the PDB policy.
I have not searched for actual examples but one could also imagine a C2
axis going through the S-S bond of a disulfide protein dimer.
To publish, we plan to provide a structure file with the correct -
higher symmetry - space group and the corresponding refinement
statistics as supporting information, in addition to the PDB deposition
in the lower symmetry space group.
Best wishes,
Ivan Huc
--
Prof. Ivan Huc
Chair of Chemical Biology - Department of Pharmacy
Institute for Chemical Epigenetics (ICE-M)
Ludwig-Maximilians-Universität
Butenandtstraße 5-13, D-81377 Munich - Germany
Office: L2.007
Tel. +49-89-2180-77804
Cel. +49-17-2778-6362
Email: [email protected]
web: https://huc.cup.uni-muenchen.de/
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