E. coli uridine phosphorylase: thymidine phosphate complex

Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium

This structure consists of eighteen monomers, all of which are in the closed conformation containing substrate (thymidine and phosphate). Due to the large size of the model it was refined using a template model, and shell scripts were written to create the 18 monomer model from this input model using the ncs operators relating each monomer to the template. The 18 monomer model was then refined using refmac5 and ncs restraints were applied as a tight positional (0.05A) and loose thermal (5.0A3) restraints. These restraints, along with tls restraints where each monomer was treated as a separate tls domain, were applied with each monomer being restrained against the template model.

TRIS HCL, PEG4000, POTASSIUM ACETATE, THYMIDINE, POTASSIUM PHOSPHATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K

UP 5-FLUOROURACIL RIBOSE-1-PHOSPHATE COMPLEX

TLS AND RESTRAINED REFINEMENT WAS CARRIED OUT USING REFMAC5.ALL 18 MONOMERS WERE REFINED USING NCS RESTRAINTS (TIGHT POSITIONAL (0.05A) AND LOOSE THERMAL (5.0A3) RESTRAINTS), AND EACH MONOMER WAS A SINGLE TLS DOMAIN.
A SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.
pentosyltransferase, uridine phosphorylase, thymidine, induced fit, specificity, potassium, TRANSFERASE