2q52: Difference between revisions
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[[Image:2q52.jpg|left|200px]] | [[Image:2q52.jpg|left|200px]] | ||
'''Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria''' | {{Structure | ||
|PDB= 2q52 |SIZE=350|CAPTION= <scene name='initialview01'>2q52</scene>, resolution 1.380Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= | |||
|GENE= c503_101305g25.t1, MSU_Galdi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=130081 Galdieria sulphuraria]) | |||
}} | |||
'''Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2Q52 is a [ | 2Q52 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Galdieria_sulphuraria Galdieria sulphuraria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q52 OCA]. | ||
==Reference== | ==Reference== | ||
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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17850744 17850744] | ||
[[Category: Galdieria sulphuraria]] | [[Category: Galdieria sulphuraria]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: Levin, E J.]] | [[Category: Levin, E J.]] | ||
[[Category: Wesenberg, G E.]] | [[Category: Wesenberg, G E.]] | ||
[[Category: center for eukaryotic structural | [[Category: center for eukaryotic structural genomic]] | ||
[[Category: cesg]] | [[Category: cesg]] | ||
[[Category: ensemble refinement]] | [[Category: ensemble refinement]] | ||
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[[Category: psi]] | [[Category: psi]] | ||
[[Category: refinement methodology development]] | [[Category: refinement methodology development]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
[[Category: unknown function]] | [[Category: unknown function]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:21:48 2008'' | ||
Revision as of 19:21, 20 March 2008
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| , resolution 1.380Å | |||||||
|---|---|---|---|---|---|---|---|
| Gene: | c503_101305g25.t1, MSU_Galdi (Galdieria sulphuraria) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria
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
2Q52 is a Protein complex structure of sequences from Galdieria sulphuraria. 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 Thu Mar 20 18:21:48 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Galdieria sulphuraria
- Protein complex
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- Center for eukaryotic structural genomic
- Cesg
- Ensemble refinement
- Gltp superfamily
- Gltp-like
- Protein structure initiative
- Psi
- Refinement methodology development
- Structural genomic
- Unknown function