Hi Priscalla and Flip, I did not bother to find out what format the maps had, I just loaded them in coot with no problems. I fitted a cyclohexane ring with three atoms attached to it (see attached pdb). It fits quite well, but there are two cautions:
1) it is impossible to deduce the type of atoms from this map, so the carbons may be oxygen, nitrogen, whatever. 2) The molecule might have a disordered attachment or binding mode and may be larger as what is fitted. It will be a nice puzzle to find out (biochemically, literature) what exactly is bound, but it is clearly some ligand molecule and not PEG. Good luck! Herman -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Priscila Oliveira de Giuseppe Sent: Friday, October 01, 2010 4:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unknown density Hi Flip, Following your suggestion, I send the link to download the screenshots of the ligand density: http://twitpic.com/2tn35i Best regards Priscila ________________________________________ From: Flip Hoedemaeker [fhoe...@googlemail.com] On Behalf Of Flip Hoedemaeker [f...@formulatrix.com] Sent: Friday, October 01, 2010 9:18 AM To: Priscila Oliveira de Giuseppe Subject: Re: [ccp4bb] unknown density Hi Priscilla, I don't think a lot of people will take the trouble to find out for themselves which format your map files have... Its better to send screen shots, better still to put your screenshots on a social media page (facebook, twitpic, whatever) and email the link. Flip On 10/1/2010 13:12, Priscila Oliveira de Giuseppe wrote: > Hi, everyone, > > I solved a structure at 1.7 A. After fitting all residues into the > model, I found an extra density at the catalytic site. The components > of the crystallization condition did not explain it (crystallization > condition: 40% PEG200, 0.1 M Tris-HCl, protein buffer: PBS) > > Neither substrates nor products of this enzyme fitted this density. > > I modelled two PEG molecules with half occupancy. They fitted very well, but I am not convinced that this is the best explanation. > > Does anyone figure out what this density can be? Attached to this e-mail I send the maps and a pdb file with the residues surrounding the ligand density. > > > > Thanks > > Priscila
UKN.pdb
Description: UKN.pdb
