I¹d like help in interpreting some mystery density in a structure. I¹m writing a paper about soaking the apo-estrogen receptor with different ligands. The apo structure is already released, as pdb code 2B23. The question is whether there is a mystery molecule in the pocket of the apo receptor. If you superimpose 3ERD, you can see where the ligand binds. The problem is that with some maps the pocket appears completely empty, and with others, there appears to be something there. Protein looks essentially identical with the different maps. We have used a few different approaches to identify the compound with LC-MS, and are pretty sure there is nothing there. For example, we can bind our protein to beads, soak it with estradiol, wash extensively, elute with organic solvent and find a great peak for estradiol, but nothing for the apo protein. We have also tried non-denaturing MS.
If you look at the 2mFo-DFc map from EDS in Coot or CCP4mg, you see mystery density in the pocket. If I use the MTZ, you see density in Coot, but not CCP4MG. I then downloaded the structure factors from the PDB and made an MTZ. The map in CCP4MG shows some density, but much less that with the map from EDS. When I used FFT to make a 2mF1-1nF2 map, there is no mystery density in either CCP4MG or coot. I was ready to submit the manuscript with a picture of the mystery density, but now I¹m not sure if that is appropriate. Any suggestions, as far as how to interpret this mystery density would be greatly appreciated. Best Regards, Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566
