This conversation brings up the question of whether it would be good practice to always do a fluorescence scan of a crystal sample, whether it is known to be a metalloprotein or not...
Energy dispersive X-ray fluorescence spectra (accessible at most synchrotron sources at this point) can often tell you whether there is metal in your sample and, because the transitions are element specific, what the metal identity is (although it can't place the metal - you need the anomalous difference for that). Note also there is a recent paper out in JACS using PIXE to investigate metalloproteins in the PDB which resolved a number of misidentified or missing metal atoms in the structures: High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application J. Am. Chem. Soc. 2020, 142, 1, 185-197 https://doi.org/10.1021/jacs.9b09186 Metals are everywhere!! Cheers, Sarah Sarah EJ Bowman, PhD Associate Research Scientist, Hauptman-Woodward Medical Research Institute Director, High-Throughput Crystallization Screening Center Research Associate Professor, Department of Biochemistry, University at Buffalo Research Webpage<https://hwi.buffalo.edu/scientist-directory/sbowman/> www.getacrystal.org<http://www.getacrystal.org> [email protected]<mailto:[email protected]> 716-898-8623 From: CCP4 bulletin board <[email protected]> on behalf of Christian Roth <[email protected]> Reply-To: Christian Roth <[email protected]> Date: Wednesday, January 22, 2020 at 12:17 PM To: "[email protected]" <[email protected]> Subject: Re: Unusual monomer-monomer interface in crystal 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
