|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2q4m' size='340' side='right'caption='[[2q4m]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2q4m' size='340' side='right'caption='[[2q4m]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q4m]] 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=2Q4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q4m]] 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=2Q4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zxu|1zxu]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At5g01750, T20L15.20 ([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=2q4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4m OCA], [https://pdbe.org/2q4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4m RCSB], [https://www.ebi.ac.uk/pdbsum/2q4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4m 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=2q4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4m OCA], [https://pdbe.org/2q4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4m RCSB], [https://www.ebi.ac.uk/pdbsum/2q4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/LOR15_ARATH LOR15_ARATH]] Might be related to the phospholipid scramblase and tubby-like superfamily of membrane tethered transcription factors.<ref>PMID:19010806</ref>
| + | [https://www.uniprot.org/uniprot/LOR15_ARATH LOR15_ARATH] Might be related to the phospholipid scramblase and tubby-like superfamily of membrane tethered transcription factors.<ref>PMID:19010806</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 35: |
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: At5g01750]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: Pfam pf01167]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Tulp]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
LOR15_ARATH Might be related to the phospholipid scramblase and tubby-like superfamily of membrane tethered transcription factors.[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
- ↑ Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Soding J. Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics. 2009 Jan 15;25(2):159-62. doi: 10.1093/bioinformatics/btn595., Epub 2008 Nov 13. PMID:19010806 doi:http://dx.doi.org/10.1093/bioinformatics/btn595
- ↑ 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
|
