Hi Chris, it could be all Ni besides Zn. I've seen Ni carried over from the initial metal affinity chromatography I presume.
Cheers Christian Chris Fage <fage...@gmail.com> schrieb am Di., 21. Jan. 2020, 21:23: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
