Hmm - if the residues are numbered sequentially and the CSO is labelled in
the dictionary as a peptide doesn't the peptide link get made internally in
the refinement programs?
Eleanor
On Tue, 8 Oct 2024 at 09:20, Kelvin Lau <
00005aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:
> I find that moving between Coot and Phenix sometimes there are issues. To
> refine in Phenix and for the links to hold in Coot I had to make custom
> links that survive both programs.
>
>
>
> An Example is below, it’s a Ligand-Cys bond, it’s a S-S bond but since its
> not part of a canonical amino acid its not recognized. You have to first
> define what the linked atoms are and then define the bond parameters.
>
>
>
> Have you tried to in phenix to make a cif-link.params file:
>
>
>
> Ie
>
>
>
> refinement.pdb_interpretation.apply_cif_link {
>
> data_link = LIG-CYS
>
> residue_selection_1 = chain X and resname LIG and resid 702 and name S15
>
> residue_selection_2 = chain C and resname CYS and resid 434 and name SG
>
> }
>
>
>
> refinement.pdb_interpretation.apply_cif_link {
>
> data_link = LIG-CYS
>
> residue_selection_1 = chain Y and resname LIG and resid 702 and name S15
>
> residue_selection_2 = chain A and resname CYS and resid 434 and name SG
>
> }
>
>
>
> refinement.pdb_interpretation.apply_cif_link {
>
> data_link = LIG-CYS
>
> residue_selection_1 = chain Z and resname LIG and resid 702 and name S15
>
> residue_selection_2 = chain B and resname CYS and resid 434 and name SG
>
> }
>
>
>
> And then to definie a new type of data_link.cif that isn’t in the database?
>
>
>
> data_link_LIG-CYS
>
> #
>
> loop_
>
> _chem_link_bond.link_id
>
> _chem_link_bond.atom_1_comp_id
>
> _chem_link_bond.atom_id_1
>
> _chem_link_bond.atom_2_comp_id
>
> _chem_link_bond.atom_id_2
>
> _chem_link_bond.type
>
> _chem_link_bond.value_dist
>
> _chem_link_bond.value_dist_esd
>
> LIG-CYS 1 S15 2 SG single 2.031 0.020
>
> loop_
>
> _chem_link_angle.link_id
>
> _chem_link_angle.atom_1_comp_id
>
> _chem_link_angle.atom_id_1
>
> _chem_link_angle.atom_2_comp_id
>
> _chem_link_angle.atom_id_2
>
> _chem_link_angle.atom_3_comp_id
>
> _chem_link_angle.atom_id_3
>
> _chem_link_angle.value_angle
>
> _chem_link_angle.value_angle_esd
>
> LIG-CYS 1 C14 1 S15 2 SG 110.000 3.000
>
> LIG-CYS 1 S15 2 SG 2 CB 110.000 3.000
>
> loop_
>
> _chem_link_tor.link_id
>
> _chem_link_tor.id
>
> _chem_link_tor.atom_1_comp_id
>
> _chem_link_tor.atom_id_1
>
> _chem_link_tor.atom_2_comp_id
>
> _chem_link_tor.atom_id_2
>
> _chem_link_tor.atom_3_comp_id
>
> _chem_link_tor.atom_id_3
>
> _chem_link_tor.atom_4_comp_id
>
> _chem_link_tor.atom_id_4
>
> _chem_link_tor.value_angle
>
> _chem_link_tor.value_angle_esd
>
> _chem_link_tor.period
>
> LIG-CYS ss 1 C14 1 S15 2 SG 2 CB 90.00 10.0 2
>
> #
>
>
>
> --
> Kelvin Lau
>
> https://people.epfl.ch/kelvin.lau
>
>
> Scientist - Protein production and structure core facility – PTPSP
>
> President – ACIDE
>
>
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin....@epfl.ch <kelvin....@epfl.ch>
> Phone: +41 21 69 30267 <+41%2021%2069%C2%A030267>
>
> If unreachable: +41 21 69 34494 <+41%2021%2069%C2%A030267>
>
>
>
>
>
> On 08.10.2024, 07:54, "Mailing list for users of COOT Crystallographic
> Software on behalf of Michelle Miller" <COOT@JISCMAIL.AC.UK on behalf of
> 0000eb408161463a-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
>
> Thanks, Keitaro – that indeed solves my first problem!
>
>
>
> Unfortunately, the fix doesn’t seem to be quite as simple for the second
> problem.
>
>
>
> *From: *Keitaro Yamashita <keitaro-yamash...@g.ecc.u-tokyo.ac.jp>
> *Date: *Tuesday, 8 October 2024 at 4:03 pm
> *To: *Michelle Miller <mille...@wehi.edu.au>
> *Cc: *COOT@jiscmail.ac.uk <COOT@jiscmail.ac.uk>
> *Subject: *Re: Help with linking two amino acid side-chains
>
> 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
> <0000eb408161463a-dmarc-requ...@jiscmail.ac.uk> 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 mille...@wehi.edu.au
> >
> >
> >
> >
> > Walter and Eliza Hall Institute of Medical Research
> > 1G Royal Parade Parkville Victoria 3052 Australia
> >
> > www.wehi.edu.au
> >
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> >
> >
> >
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