Dear Prescilla, Hermans suggestion look pretty convincing. Try to refine it and see if the difference density disappears. I'd replace the C8 atom with oxygen because you need it to coordinate the magnesium ion. The residue near C11 can also tell you whether that atom chould be polar or not. I'm guessing it's a HIS so the C11 atom should be a hydrogen bond donor or acceptor. The Residue next to the HIS (ASP or ASN) may tell you more about the protonation of the HIS. This is a fun game. Cheers, Robbie Joosten
---------------------------------------- > Date: Fri, 1 Oct 2010 17:21:31 +0200 > From: herman.schreu...@sanofi-aventis.com > Subject: Re: [ccp4bb] unknown density > To: CCP4BB@JISCMAIL.AC.UK > > 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
