Hi all, We have recently solved a structure of a DNA binding protein in complex with DNA to ca 2.5 Å. The space group is P212121 and contains 3 protein molecules in the asymmetric unit (current Rwork/Rfree = 20.4/24.1). The protein was crystallized together with a 60 bases long poly-A oligo (ssDNA). Each protein molecule binds to a stretch of this DNA. However, only 15 bp of the DNA is part of the asymmetric unit, with each protein molecule binding 5 bp. The DNA then goes on to the next ASU (with its 3 proteins) and so forth. There is no sequence specificity to the DNA, so it can “slide”. Redoing the structure in P1 does not really help, as due to its “sliding” nature the density is still continuous in between ASUs.
Currently, the structure model thus consists of 3 protein molecules and one 15 bases long DNA. However, the density for the DNA is as I wrote continuous into the neighboring ASUs. Any advice for how to deal with this in the model would be most welcome! We can of course explain it in the manuscript that we’ll submit, but would feel good if one can represent it in a better way also in the pdb. Hopefully I’ve managed to convey my question here, but let me know if any clarification is needed. Best wishes, Ronnie ---------- Ronnie Berntsson, PhD Chair of the Young Academy of Sweden Department of Medical Biochemistry and Biophysics, Umeå University 90187 Umeå, Sweden e-mail: ronnie.bernts...@umu.se<mailto:ronnie.bernts...@umu.se> phone: +46 90 7865235<tel:+46907865235> web: https://www.biostruct.umu.se/principal-investigators/ronnie-berntsson/ ######################################################################## 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/
