1sx2
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Use of a Halide Binding Site to Bypass the 1000-atom Limit to Structure Determination by Direct Methods
OverviewOverview
Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic, groups are very difficult to solve by ab initio direct methods. T4, lysozyme is being used to explore these limits. The protein has 1309 non-H, atoms, seven S atoms, no disulfide bonds and no heavy-atom prosthetic, group. It is recalcitrant to structure determination by direct methods, using X-ray diffraction data to 0.97 A. It is shown here that it is, possible to obtain a truly ab initio structure determination of a variant, of the protein that has an Rb+ (Z = 37) binding site. Using diffraction, data to 1.06 A resolution, the direct-methods programs SIR2002 and ACORN, independently solved the structure in about 20 h. The bound Rb+, which, contributes about 1.7% of the total scattering, does not appear to distort, the structure or to inhibit refinement (R factor 12.1%). The phases, obtained via SIR2002 or ACORN are in good agreement with those from a, reference structure obtained from conventional molecular-substitution and, refinement procedures (average error in the figure-of-merit-weighted, phases of less than 25 degrees). Thus, proteins with more than 1000 atoms, that include halide-binding or other such sites may be amenable to, structure determination by ab initio direct methods. The direct-methods, approaches are also compared with structure determination via use of the, anomalous scattering of the Rb+ ion. As shown by examples, high-resolution, structures determined by direct methods can be useful in highlighting, regions of strain in the protein, including short hydrogen bonds and, non-planar peptide groups.
About this StructureAbout this Structure
1SX2 is a Single protein structure of sequence from Bacteriophage t4 with RB, CL and BME as ligands. Active as Lysozyme, with EC number 3.2.1.17 Full crystallographic information is available from OCA.
ReferenceReference
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods., Mooers BH, Matthews BW, Acta Crystallogr D Biol Crystallogr. 2004 Oct;60(Pt 10):1726-37. Epub 2004, Sep 23. PMID:15388918
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