2q3u: Difference between revisions
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'''Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase''' | {{Structure | ||
|PDB= 2q3u |SIZE=350|CAPTION= <scene name='initialview01'>2q3u</scene>, resolution 1.530Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> and <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE SULFONIC ACID'>MPO</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] | |||
|GENE= AIH, At5g08170, T22D6.110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | |||
}} | |||
'''Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2Q3U is a [ | 2Q3U 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=2Q3U 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: Agmatine deiminase]] | [[Category: Agmatine deiminase]] | ||
[[Category: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
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[[Category: aih]] | [[Category: aih]] | ||
[[Category: at5g08170]] | [[Category: at5g08170]] | ||
[[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: putrescine]] | [[Category: putrescine]] | ||
[[Category: refinement methodology development]] | [[Category: refinement methodology development]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
''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 18:21:17 2008'' | ||
Revision as of 19:21, 20 March 2008
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| , resolution 1.530Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | AIH, At5g08170, T22D6.110 (Arabidopsis thaliana) | ||||||
| Activity: | Agmatine deiminase, with EC number 3.5.3.12 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase
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
2Q3U 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 Thu Mar 20 18:21:17 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Agmatine deiminase
- Arabidopsis thaliana
- Single protein
- CESG, Center for Eukaryotic Structural Genomics.
- Jr., G N.Phillips.
- Kondrashov, D A.
- Levin, E J.
- Wesenberg, G E.
- EDO
- MG
- MPO
- Agmatine iminohydrolase
- Aih
- At5g08170
- Center for eukaryotic structural genomic
- Cesg
- Ensemble refinement
- N-carbamoylputrescine
- Polyamine biosynthesis
- Protein structure initiative
- Psi
- Putrescine
- Refinement methodology development
- Structural genomic