2q3u: Difference between revisions
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|GENE= AIH, At5g08170, T22D6.110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana]) | |GENE= AIH, At5g08170, T22D6.110 ([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=pfam04371 PAD_porph]</span> | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam04371 PAD_porph]</span> | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.ebi.ac.uk/pdbsum/2q3u PDBsum | |RELATEDENTRY=[[1vkp|1vkp]] | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB]</span> | |||
}} | }} | ||
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[[Category: structural genomic]] | [[Category: structural genomic]] | ||
''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 04:44:14 2008'' | ||
Revision as of 04:44, 31 March 2008
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| , resolution 1.530Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | AIH, At5g08170, T22D6.110 (Arabidopsis thaliana) | ||||||
| Activity: | Agmatine deiminase, with EC number 3.5.3.12 | ||||||
| Domains: | PAD_porph | ||||||
| Related: | 1vkp
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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
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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.
- 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