ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE TRANSGLYCOSYLASE USING WARP/

The X-ray structure of the 36 kDa soluble lyric transglycosylase from Escherichia coli has been determined starting with the multiple isomor phous replacement method with inclusion of anomalous scattering at 2.7 Angstrom resolution. Subsequently, before any model building was carr ied out, phases were extended to 1.7 Angstrom resolution with the weig hted automated refinement procedure wARP, which gave a dramatic improv ement in the phases. The electron-density maps from wARP were of outst anding quality for both the main chain and the side chains of the prot ein, which allowed the time spent on the tracing, interpretation and b uilding of the X-ray structure to be substantially shortened. The stru cture of the soluble lyric transglycosylase was refined at 1.7 Angstro m A resolution with X-PLOR to a final crystallographic R factor of 18. 9%. Analysis of the wARP procedure revealed that the use of the maximu m-likelihood refinement in wARP gave much better phases than least-squ ares refinement, provided that the ratio of reflections to protein ato m parameters was approximately 1.8 or higher. Furthermore, setting asi de 5% of the data for an R-free test set had a negative effect on the phase improvement. The mean W-wARP a weight determined at the end of t he wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the R-free factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly alpha-helices, whi le the beta domain consists of a five-stranded antiparallel beta-sheet flanked by a short alpha-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble ly ric transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.