|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2q4y' size='340' side='right'caption='[[2q4y]], [[Resolution|resolution]] 2.06Å' scene=''> | | <StructureSection load='2q4y' size='340' side='right'caption='[[2q4y]], [[Resolution|resolution]] 2.06Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q4y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q4y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.06Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2il4|2il4]], [[1xmt|1xmt]], [[2evn|2evn]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g77540, T5M16.13 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4y OCA], [https://pdbe.org/2q4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4y RCSB], [https://www.ebi.ac.uk/pdbsum/2q4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4y ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4y OCA], [https://pdbe.org/2q4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4y RCSB], [https://www.ebi.ac.uk/pdbsum/2q4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4y ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/Y1754_ARATH Y1754_ARATH]] Possesses in vitro histone acetyltransferase activity with histones H3 and H4.<ref>PMID:17128971</ref>
| + | [https://www.uniprot.org/uniprot/Y1754_ARATH Y1754_ARATH] Possesses in vitro histone acetyltransferase activity with histones H3 and H4.<ref>PMID:17128971</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 34: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Kondrashov DA]] |
| - | [[Category: Kondrashov, D A]] | + | [[Category: Levin EJ]] |
| - | [[Category: Levin, E J]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Phillips, G N]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: Wesenberg, G E]] | + | |
| - | [[Category: Acetyltransferase]]
| + | |
| - | [[Category: At1g77540]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Coa]]
| + | |
| - | [[Category: Coenzyme-a]]
| + | |
| - | [[Category: Cog2388 family]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
Y1754_ARATH Possesses in vitro histone acetyltransferase activity with histones H3 and H4.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tyler RC, Bitto E, Berndsen CE, Bingman CA, Singh S, Lee MS, Wesenberg GE, Denu JM, Phillips GN Jr, Markley JL. Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry. 2006 Dec 5;45(48):14325-36. PMID:17128971 doi:10.1021/bi0612059
- ↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019
|
