2q4h
From Proteopedia
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| - | [[Image:2q4h.jpg|left|200px]] | + | [[Image:2q4h.jpg|left|200px]] |
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| - | '''Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200''' | + | {{Structure |
| + | |PDB= 2q4h |SIZE=350|CAPTION= <scene name='initialview01'>2q4h</scene>, resolution 1.834Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/UDP-glucose--hexose-1-phosphate_uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.12 2.7.7.12] | ||
| + | |GENE= AT5G18200, MRG7_16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | ||
| + | }} | ||
| + | |||
| + | '''Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2Q4H is a [ | + | 2Q4H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4H 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: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: ZN]] | [[Category: ZN]] | ||
[[Category: amp]] | [[Category: amp]] | ||
| - | [[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: transferase]] | [[Category: transferase]] | ||
[[Category: zinc]] | [[Category: zinc]] | ||
| - | ''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 18:21:35 2008'' |
Revision as of 16:21, 20 March 2008
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| , resolution 1.834Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | AT5G18200, MRG7_16 (Arabidopsis thaliana) | ||||||
| Activity: | UDP-glucose--hexose-1-phosphate uridylyltransferase, with EC number 2.7.7.12 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200
Overview
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 Structure
2Q4H is a Single protein structure of sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA.
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:17850744
Page seeded by OCA on Thu Mar 20 18:21:35 2008
Categories: Arabidopsis thaliana | Single protein | UDP-glucose--hexose-1-phosphate uridylyltransferase | CESG, Center for Eukaryotic Structural Genomics. | Jr., G N.Phillips. | Kondrashov, D A. | Levin, E J. | Wesenberg, G E. | AMP | EDO | ZN | Amp | Center for eukaryotic structural genomic | Cesg | Ensemble refinement | Galt | Protein structure initiative | Psi | Refinement methodology development | Structural genomic | Transferase | Zinc
