2Q4J
Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase
Summary for 2Q4J
| Entry DOI | 10.2210/pdb2q4j/pdb |
| Related | 2ICX 2ICY |
| Descriptor | Probable UTP-glucose-1-phosphate uridylyltransferase 2 (2 entities in total) |
| Functional Keywords | ensemble refinement, refinement methodology development, at3g03250, putative udp-glucose pyrophosphorylase, structural genomics, protein structure initiative, psi, center for eukaryotic structural genomics, cesg, transferase |
| Biological source | Arabidopsis thaliana (thale cress) |
| Cellular location | Cytoplasm (By similarity): Q9M9P3 |
| Total number of polymer chains | 2 |
| Total formula weight | 103596.41 |
| Authors | Levin, E.J.,Kondrashov, D.A.,Wesenberg, G.E.,Phillips Jr., G.N.,Center for Eukaryotic Structural Genomics (CESG) (deposition date: 2007-05-31, release date: 2007-06-19, Last modification date: 2023-08-30) |
| Primary citation | Levin, E.J.,Kondrashov, D.A.,Wesenberg, G.E.,Phillips, G.N. Ensemble refinement of protein crystal structures: validation and application. Structure, 15:1040-1052, 2007 Cited by PubMed Abstract: X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement. PubMed: 17850744DOI: 10.1016/j.str.2007.06.019 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.863 Å) |
Structure validation
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