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RE: [ccp4bb]: Uranile coordination



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Dear Marie Helene,

That seems an interesting but slightly dangerous idea. The danger is that uranyl often binds to many sites and causes non-isomorphism. Possibly recent programs such as SHARP and SOLVE can give reliable descriptions of the uranyl binding but older studies may not have found all the uranyl sites and may have included some false sites. This happened to me in the two cases that I checked. I mentioned in Jenkins et al. J. Mol. Biol. 305, 951-960, 2001 to justify using 12 sites
"However, examination of difference Fourier maps phased using the refined structure revealed that at least 16 uranyl sites should have been used, which were all associated with carboxylates." Similarly the description of the uranyl sites in pectin lyase contained errors, which were only discovered after publication.

Thus I think you should either be asking for the structure factors or should only use the high occupancy sites or perhaps only use very recent structures. 

I am less sure of this but is it possible to get a distorted picture of the coordination from the PDB file and the fractional coordinates of the uranyl site if the derivative is non-isomorphous?

Best wishes

John Jenkins

Institute of Food Research     	Tel:   +44 (0)1603 255319
Norwich Research Park          	Fax:   +44 (0)1603 507723
Colney Lane                    	E-mail john.jenkins@bbsrc.ac.uk
Norwich NR4 7UA
UK


-----Original Message-----
From: Marie Helene Le Du [mailto:mhledu@cea.fr]
Sent: 22 October 2002 10:00
To: CCP4
Subject: [ccp4bb]: Uranile coordination


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Dear users,

My question is not directly related to CCP4, but it needs the help of
the entire
community of protein crystallographers.
We are studying the coordination of uranium in proteins, and because of
its large
used for heavy atom derivative search, we would like to build a library
of the coordination
observed in protein crystals.
Therefore, we would be very pleased if the people who have used
successfully an uranyl salt
to solve their structure could send us a short mail with the pdb entry
of the protein, the
coordinate of the uranyl in the structure, and the uranyl salt used.
If there is some general interest for this information, we may extend it
to other heavy
atoms, and give access to our results.

Thanks in advance,

Marie Helene Le Du 

-- 
Dr. Marie Helene Le Du  
Departement d'Ingenierie et d'Etude des Proteines           
Bat 152 C.E. Saclay           
91191 Gif-sur-Yvette 
tel : (33) (0)1 69 08 71 35 	fax : (33) (0)1 69 08 90 71