Good luck with the deposition!

And if you later manage to identify this ligand, the PDB allows updating an 
already processed and released entry with a new atomic model, without changing 
the accession code. It is a relatively simple process if you saved the 
deposition ID and password, even easier if you logged into the deposition 
system with your ORCiD (then all the depositions linked to it will be listed).

More info here: https://www.rcsb.org/news/feature/5910c8d8d3b1d333029d4ea8


I hope this helps,


Guillaume

________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Ekaterina Kot 
<0000f9b81f2028a5-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, December 17, 2024 9:58:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: 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 <ddas.cons...@gmail.com>
Sent: 16 December 2024 20:22
To: Ekaterina Kot <ekaterina....@magd.ox.ac.uk>
Cc: CCP4BB@jiscmail.ac.uk
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 
<0000f9b81f2028a5-dmarc-requ...@jiscmail.ac.uk<mailto:0000f9b81f2028a5-dmarc-requ...@jiscmail.ac.uk>>
 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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