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2q51
From Proteopedia
| 2q51, resolution 2.80Å () | |||||||||
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| Sites: | , , , , , , , , and | ||||||||
| Ligands: | , | ||||||||
| Non-Standard Residues: | |||||||||
| Gene: | ASPA, ACY2, ASP (Homo sapiens) | ||||||||
| Activity: | Aspartoacylase, with EC number 3.5.1.15 | ||||||||
| Related: | 2i3c, 2gu2 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens
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.
Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:17850744
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2q51 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
- Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:10.1016/j.str.2007.06.019
- Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr. Structure of aspartoacylase, the brain enzyme impaired in Canavan disease. Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):456-61. Epub 2006 Dec 28. PMID:17194761
Categories: Aspartoacylase | Homo sapiens | CESG, Center for Eukaryotic Structural Genomics. | Kondrashov, D A. | Levin, E J. | Phillips, G N. | Wesenberg, G E. | Acy2 | Aminoacylase-2 | Aspa | Aspartoacylase family | Canavan disease | Center for eukaryotic structural genomic | Cesg | Ensemble refinement | Hydrolase | N-acetyl-l-aspartate | Protein structure initiative | Psi | Refinement methodology development | Structural genomic | Zinc-dependent hydrolase
