It could be purine or pyrimidine ring stacked between the Phe an Tyr. check pdb 3etr or 3eub of xanthine oxidase binding purine substrates between two Phe at the active site. Hongnan Cao UCR
Date: Tue, 10 Feb 2009 00:23:54 -0500From: lvmengx...@gmail.comsubject: [ccp4bb] unknown density for a small moleculeTo: ccp...@jiscmail.ac.ukdear All,When I was refining my structure, I found some unmodeled blobs, shown as attached images (contoured at 3 sigma for Fo-Fc, Rfree 0.21 and Rfactor 0.18, refined to 1.9 angstrom ). The protein was expressed in E.coli and purified by nickel column and gel filtration, both in tris buffer. The crystallization condition has 2 M ammonium sulfate and 0.1 M sodium acetate. The lower part looks like a sulfate group, which is held by one Arg, one his, one lys and one asn. The latter three residues are from another asymmetric unit. The other end of the small molecule is stunk by the rings of Tyr and Phe. It also interacts with the OH group of another tyr and one water molecule. Is there a program can build small molecule models according to the densities? Or could anyone tell what it might be from the density? Thanks a lot! Any suggestions will be appreciated!Mengxiao _________________________________________________________________ 上Windows Live 中国首页，下载最新版 MSN！ http://im.live.cn/
