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 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 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/
