2q4d: Difference between revisions
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|GENE= AT5G11950, F14F18.120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | |GENE= AT5G11950, F14F18.120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | ||
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03641 Lysine_decarbox]</span> | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03641 Lysine_decarbox]</span> | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4d OCA], [http://www.ebi.ac.uk/pdbsum/2q4d PDBsum | |RELATEDENTRY=[[1ydh|1YDH]], [[2a33|2A33]] | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4d OCA], [http://www.ebi.ac.uk/pdbsum/2q4d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q4d RCSB]</span> | |||
}} | }} | ||
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[[Category: unknown function]] | [[Category: unknown function]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:44:32 2008'' | ||
Revision as of 04:44, 31 March 2008
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| , resolution 2.152Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | AT5G11950, F14F18.120 (Arabidopsis thaliana) | ||||||
| Domains: | Lysine_decarbox | ||||||
| Related: | 1YDH, 2A33
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950
OverviewOverview
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.
About this StructureAbout this Structure
2Q4D is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.
ReferenceReference
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
Page seeded by OCA on Mon Mar 31 04:44:32 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Arabidopsis thaliana
- Single protein
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- At5g11950
- Center for eukaryotic structural genomic
- Cesg
- Ensemble refinement
- Lysine decarboxylase-like protein
- Protein structure initiative
- Psi
- Refinement methodology development
- Structural genomic
- Unknown function