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 >> >> >> >> >> >> [image: 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 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/
