I agree with Keitaro.
For the second issue, that should be covered in Rob's CCP4 presentation:
https://www.youtube.com/watch?v=p4oTJ0bjD3M
Paul.
On 08/10/2024 06:02, Keitaro Yamashita wrote:
Dear Michelle,
CSO is a peptide in the latest monomer library, which is included in
CCP4 9.0. I suppose you are using an old version. At least the first
issue may be sorted by using COOT from CCP4 9.0.
Best regards,
Keitaro
On Tue, 8 Oct 2024 at 13:30, Michelle Miller
<[email protected]> wrote:
Hi,
I’m trying to model a N-O-S bond between a lysine side-chain and an oxidised
cysteine (CSO) as described in
https://www.nature.com/articles/s41467-024-48109-3
I’m facing two problems in Coot (v 0.9.8.3):
Firstly, when I go >Replace residue and replace the cysteine with a CSO – Coot
does not recognise the CSO as part of the peptide chain. I can manually (roughly)
put it in place and Phenix will fix it during refinement, however this continues
to be a problem for coot.
Secondly, I have tried a couple of ways to model the NOS bond and none of them
seem to work correctly.
I defined the link using JLigand, saved the cif file and the LINK record. I
manually put this link in place in Coot, loaded the cif file into Phenix and it
sort of worked, although the O-N bond length is too long and doesn’t match what
is defined in the cif file (~1.99 Å vs 1.38 Å). Furthermore, after loading the
cif file in coot, when I try to do a real space refine, it does not recognise
the O-N link (or the CSO as part of the peptide chain as described above).
I defined the entire CSO-LYS as a ligand and generated cif restraints in Phenix
using elBOW, loaded the pdb into Coot and placed into the density, merged with
the pdb and tried to define “links” to the peptide backbone on both sides. As
above, these bonds are not recognised by coot. After running through phenix,
the planarity of the amide bonds is lost.
To add to the complexity, there are two conformations of the N-O-S
modification/linkage, so I also want to be able to model that.
Any help would be greatly appreciated!!
Thanks,
Michelle
---------------------------------------
Michelle Miller PhD
Senior Research Officer
Structural Biology
E [email protected]
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade Parkville Victoria 3052 Australia
www.wehi.edu.au
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