2Q3S

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g06450

Summary for 2Q3S

• Entry DOI: 10.2210/pdb2q3s/pdb
• Descriptor: Protein At5g06450 (2 entities in total)
• Functional Keywords: ensemble refinement, refinement methodology development, protein, homohexamer, at5g06450, structural genomics, protein structure initiative, psi, center for eukaryotic structural genomics, cesg, unknown function
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 6
• Total formula weight: 139458.44

Authors

Levin, E.J.,Kondrashov, D.A.,Wesenberg, G.E.,Phillips Jr., G.N.,Center for Eukaryotic Structural Genomics (CESG) (deposition date: 2007-05-30, release date: 2007-06-19, Last modification date: 2024-10-30)

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

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: 17850744
DOI: 10.1016/j.str.2007.06.019

Experimental method

X-RAY DIFFRACTION (2.1 Å)