2Q41
Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820
Summary for 2Q41
| Entry DOI | 10.2210/pdb2q41/pdb |
| Descriptor | Spermidine synthase 1 (2 entities in total) |
| Functional Keywords | ensemble refinement, refinement methodology development, at1g23820, putrescine aminopropyl transferase, spermidine synthase, spds1, polyamine, structural genomics, protein structure initiative, psi, center for eukaryotic structural genomics, cesg, transferase |
| Biological source | Arabidopsis thaliana (thale cress) |
| Total number of polymer chains | 4 |
| Total formula weight | 147685.70 |
| 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: 2024-11-13) |
| 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 (2.7 Å) |
Structure validation
Download full validation report
