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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
