Not sure I understood your problem but it looks like it's related to flexibility. You can try cutting the domains apart (and chopping off the loops) in two different pdbs. They can be used as separate ensembles. Try to find the bigger one first. 35% homology is not that low, just search with polyAla.
(You can also analyze the analogue with Normal Modes to see where it bends in case it's not obvious). Carlos Em 01/10/2012, às 21:26, RHYS GRINTER escreveu: > Hi All, > > I'm currently working on solving the structure of a protein by molecular > replacement. The protein is around 30kDa and likely has a two beta-prism > domains, linked by a long curved two stranded sheet based on the structure of > an analogue. There are also a number of other structures which represent a > single homologous beta-prism domain. > I've tried to find MR solution using the analogue and various truncation/AA > substitution models based on it with no success. I've also tried single > domain ensembles of the other homologous structures, also with no success. I > think the problem is the overall sequence homology is quite low between my > protein and the available structures (35% for the analogue and around 20% for > the other models. > > I was curious as to how someone with more experience would tackle this > problem. > > Just for background, the datasets I have are 2 to 2.7 angstroms with pretty > nice stats. The space group is most likely C2221 with two molecules per ASU > (giving around 58% solvent). > > Thanks, > > Rhys Grinter > PhD Candidate > University of Glasgow
