[buster-discuss] Big trouble with MLY

[Kikuti Carlos]

Hello !

Here I go asking for help again…

I’m finishing the refinement of a ~800 residues structure at 2.4 angstroms, the protein sample was extracted from an animal, it has a few PTMs, especially on lysine side chains. I’m used to placing M3L and running Buster on them, no problems. But now with this new protein, when I place a dimethyl-lysine (MLY) as amino acid 189, something very strange happens (and I tried this twice already):

  1.  Buster places a TER line just upstream to the MLY residue
  2.  The PDB Validate server interprets everything downstream to aa 188 as HETATM, so all the peptide bonds are considered as clashes – funny enough, on Coot everything looks perfectly fine, Rama and planarity of the two peptide bonds around the modified lysine are fine…
My detailed protocol for adding modified residues like this one is:

  1.  Delete the original LYS
  2.  Coot: File->Get Monomer… MLY
  3.  Place it in the density, do some real space refinement
  4.  Delete OXT, H1 and H2 (otherwise the peptide bond gets 3 hydrogens bound to the N).
  5.  Edit->Merge Molecules… (this usually gives the right chain name to the residue already)
  6.  Edit->Renumber Residues… to put it in the sequence
  7.  Real space refinement again, to get the peptide bond correct.
I am sure it is Buster, and not Coot, adding the TER line.
I also tried producing new restrains for MLY with Grade and running Buster with AnalyseGellySanityCheckForDuplicateBonds=no – but the TER line still appears
Of course I can cheat and modify the final mmcif file so that Validate will probably accept it, but I imagine there is a way to tell Buster to behave just like with M3L? We have a few similar structures that will be published in the same paper…

I hope you can help, because the other refinement programs always give worse geometry than Buster on these cases, I didn’t even try them.

Best,
---------------------------------------------------
Carlos KIKUTI, PhD
UMR144 - CNRS - Institut Curie
Pavillon Trouillet Rossignol
26 Rue d’Ulm - 75005 Paris, France
carlos.kikuti at curie.fr<mailto:carlos.kikuti at curie.fr>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20240201/d90ded73/attachment.html>