No problem, it would be interesting to refine it as a tricarboxy methane amide of the His imidazole. More info on 2-carboxyl malonic acid here:
https://pubchem.ncbi.nlm.nih.gov/compound/Methanetricarboxylic-acid Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 18 Aug 2021, 12:13, Ana Ebrecht wrote: > Hello Jon, > Thanks for the comments. Yes, the His is part of the active site, and the > distances are very close, like a covalent bond. That's why I was wondering if > the malonate can be bound to the His. > > We tried to model the malonate in the different conformation, but that didn't > work. But I'll check about the protease inhibitor. Thanks! > > Kind regards > Ana > > On Tue, 17 Aug 2021 at 14:48, Jon Cooper <[email protected]> wrote: > >> Hello, only other thought was that malonate might be binding in two >> conformations, i.e. dual occupancy, and did you use a protease inhibitor >> cocktail, since the constituents can react? The density looks a bit like >> citrate, but too close to the His. I couldn't read the distances to the His >> in your figure. Is it part of the active site and if so can you say what the >> enzyme is? Anomalous difference maps are popular here, too. Is the >> surrounding structure totally OK because odd features in the difference map >> can indicate problems nearby e.g. I did see a leucine which looked slightly >> strained on the left, but maybe I am wrong. Good luck. Cheers, Jon.C. >> >> Sent from ProtonMail mobile >> >> -------- Original Message -------- >> On 17 Aug 2021, 12:11, Ana Ebrecht < [email protected]> wrote: >> >>> Hi Jon, >>> Thanks for the reply. I don't think this is acetylation, because I only see >>> this density in the crystals that grew with malonate. In other conditions >>> doesn't show anything like that. So I thought it'd be the malonate. But >>> I'll check on that. >>> Thanks for the suggestion. >>> >>> Kind regards >>> Ana >>> >>> On Mon, 16 Aug 2021 at 16:56, Jon Cooper <[email protected]> >>> wrote: >>> >>>> Hello, could the His be partially acetylated? >>>> >>>> Best wishes Jon.C. >>>> >>>> Sent from ProtonMail mobile >>>> >>>> -------- Original Message -------- >>>> On 16 Aug 2021, 14:52, Ana Ebrecht < [email protected]> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I am building the structure of a protein that was crystallized in 0.2 M >>>>> sodium malonate pH 5.0, 20% w/v polyethylene glycol 3,350. >>>>> During the refinement, we found what we think is a malonate molecule in >>>>> the active site, but it seems like is bound somehow to the histidine >>>>> (this His is the catalytic residue of the enzyme), almost like a covalent >>>>> interaction. Under other conditions of crystallization, the protein bound >>>>> a sulfate and an acetate in the site but did not show this type of >>>>> interaction with the histidine. >>>>> >>>>> We couldn't find anything that explains a reaction between the malonate >>>>> and the histidine. >>>>> Does anyone have experience with this reaction or have seen something >>>>> similar before? >>>>> >>>>> Thanks >>>>> Kind regards >>>>> Ana >>>>> >>>>> [malonate.jpg] >>>>> >>>>> --------------------------------------------------------------- >>>>> >>>>> 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 > > --------------------------------------------------------------- > > 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 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/
