I am probably wrong, but to me it looks like PEG. Maybe a small peptide product
of degradation?
Best wishes
______________________________________________________
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +44 07861 273773
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <[email protected]> em nome de Ekaterina Kot
<[email protected]>
Enviado: terça-feira, 17 de dezembro de 2024 08:58
Para: [email protected] <[email protected]>
Assunto: Re: [ccp4bb] Modelling unidentified ligand
Hello everyone,
Thank you for all your responses. I shall try the JCSG strategy for modelling.
Some additional information which was asked for:
* Crystallisation buffer is MES and ammonium sulphate, purification buffer
is Hepes, NaCl and TCEP
* I was using the CIF file I downloaded from the pdb UNL page
https://www.rcsb.org/ligand/UNL
* I am using Refmac within CCP4i2 interface
As far as identification, thank you for suggestions as well, I shall try them
in the future but for now I would just like to deposit.
Thank you,
Kate
From: Debanu <[email protected]>
Sent: 16 December 2024 20:22
To: Ekaterina Kot <[email protected]>
Cc: [email protected]
Subject: Re: [ccp4bb] Modelling unidentified ligand
Hi Kate,
We dealt with UNLs extensively at JCSG (Joint Center for Structural Genomics)
and deposited/published numerous structures with UNL. These are cases of
presumably “endogenous” ligands, many with potential functional implications,
with unambiguous electron density that could not be attributed to purification
buffers or crystallization conditions.
How we treated them for fitting/refinement/PDB depositions can be seen in their
PDB files and also described in these two papers, including their potential
importance and consequences. Especially, see sections 2.2, 3 and 4 in the first
paper:
https://journals.iucr.org/f/issues/2010/10/00/wd5119/index.html
And an overview of the above publication in this commentary by Ben Cravatt:
https://pmc.ncbi.nlm.nih.gov/articles/PMC2954220/
Best regards,
Debanu
—
Debanu Das, Ph.D.
bio.site/debanu_das
—
On Mon, Dec 16, 2024 at 08:21 Ekaterina Kot
<[email protected]<mailto:[email protected]>>
wrote:
Hello everyone,
I am trying to build a crystal model where I have clear density of an
unidentified ligand.
I would like to deposit, but do not want to mislead as to the identity of the
atoms, therefore I’ve opted to using UNL code, but then cannot get refinement
to start.
Does anyone know the procedure for building in and refining an unidentified
ligand?
Picture for reference:
[cid:ii_193d11ccc26ad7999131]
Thank you in advance,
Kate
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