2q4t: Difference between revisions
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[[Image:2q4t.jpg|left|200px]] | [[Image:2q4t.jpg|left|200px]] | ||
'''Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936''' | {{Structure | ||
|PDB= 2q4t |SIZE=350|CAPTION= <scene name='initialview01'>2q4t</scene>, resolution 2.350Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID'>EPE</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/5'-nucleotidase 5'-nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.5 3.1.3.5] | |||
|GENE= Nt5c3, VSP_021566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | |||
}} | |||
'''Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2Q4T is a [ | 2Q4T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4T 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: 5'-nucleotidase]] | [[Category: 5'-nucleotidase]] | ||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
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[[Category: aah38029]] | [[Category: aah38029]] | ||
[[Category: bc038029]] | [[Category: bc038029]] | ||
[[Category: center for eukaryotic structural | [[Category: center for eukaryotic structural genomic]] | ||
[[Category: cesg]] | [[Category: cesg]] | ||
[[Category: cytosolic 5'-nucleotidase iii]] | [[Category: cytosolic 5'-nucleotidase iii]] | ||
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[[Category: psi]] | [[Category: psi]] | ||
[[Category: refinement methodology development]] | [[Category: refinement methodology development]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
[[Category: umph-1]] | [[Category: umph-1]] | ||
''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 18:21:41 2008'' | ||
Revision as of 19:21, 20 March 2008
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| , resolution 2.350Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | Nt5c3, VSP_021566 (Mus musculus) | ||||||
| Activity: | 5'-nucleotidase, with EC number 3.1.3.5 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936
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
2Q4T is a Single protein structure of sequence from Mus musculus. 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 18:21:41 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- 5'-nucleotidase
- Mus musculus
- Single protein
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- EPE
- Aah38029
- Bc038029
- Center for eukaryotic structural genomic
- Cesg
- Cytosolic 5'-nucleotidase iii
- Ensemble refinement
- Hydrolase
- Mm 158936
- Nt5c3 protein
- Protein structure initiative
- Psi
- Refinement methodology development
- Structural genomic
- Umph-1