2Q4X: Ensemble Refinement Of The Protein Crystal Structure Of Gene Product From Arabidopsis Thaliana At3g16990

Citation:
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.
PDB ID: 2Q4XDownload
MMDB ID: 47022
PDB Deposition Date: 2007/5/31
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Similar Structures:
Biological Unit for 2Q4X: monomeric; determined by author
Molecular Components in 2Q4X
Label Count Molecule
Protein (1 molecule)
1
Seed Maturation Protein Pm36 Homolog(Gene symbol: AT3G16990)
Molecule annotation
Chemicals (2 molecules)
1
1
2
1
* Click molecule labels to explore molecular sequence information.

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