Thanks to Guenter and Eleanor for their replies. I mentioned that there is not adequate space for a metal ion at the described interfaces. Nevertheless, placement of a metal ion, followed by refinement in Phenix, repositions the side chains significantly so as to make room for the ion without distorting geometry. There is also a very strong difference signal centered between the four side chains. This agrees with the MS data, which indicate a monomeric state without a disulfide linkage. Now, I just need to identify the metal. A Zn2+ seems to fit well based on coordination number and interatomic distances, as Guenter exemplified.
Best wishes, Chris On Tue, Jan 21, 2020 at 6:33 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > Easy to check whether it is a metal by looking at an anomalous difference > map.. > But there are examples of di-sulphides formed between symmetry related > molecules.. > Query the wwwpdb - > > > On Tue, 21 Jan 2020 at 18:06, Guenter Fritz < > guenter.fritz.phenix.c...@gmail.com> wrote: > >> Dear Chris, are there any metal ions in your buffer or in your protein. >> We had a similar looking case. A Zn2+ ion bridged two monomers. Our protein >> is a Zn2+ binding protein. The Zn2+ originated from some denatured protein >> in the drop. No extra Zn2+ was in the crystallization buffer. >> >> http://www.rcsb.org/structure/5CHT >> https://www.nature.com/articles/nsmb.3371 >> HTH >> Guenter >> >> Dear CCP4BB Users, >> >> I've recently solved the ~2.2 angstrom structure of a protein. In my >> electron density there are unusual monomer-monomer interfaces involving >> pairs of His and Cys residues (see https://ibb.co/wdWBcdk). Note the >> positive Fo-Fc density between the four side chains. As there is not >> adequate space for a water molecule or metal ion, perhaps the Cys residues >> are partially tied up disulfide bonds? However, the protein looks to be >> fully monomeric based on LC-MS measurements. Has anyone else observed >> crystal-driven formation of disulfide bridges? >> >> Aside from this region, there is no extensive interface between momoners, >> and PDBePISA suggests a monomeric state. >> >> Thanks in advance for any advice! >> >> Best wishes, >> Chris >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
