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| | ==Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260== | | ==Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260== |
| - | <StructureSection load='2q4n' size='340' side='right' caption='[[2q4n]], [[Resolution|resolution]] 1.32Å' scene=''> | + | <StructureSection load='2q4n' size='340' side='right'caption='[[2q4n]], [[Resolution|resolution]] 1.32Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q4n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q4n]] 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=2Q4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4N FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.32Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2a13|2a13]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g79260, YUP8H12R.14 ([http://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=2q4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4n OCA], [https://pdbe.org/2q4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4n RCSB], [https://www.ebi.ac.uk/pdbsum/2q4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4n ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4n OCA], [http://pdbe.org/2q4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4n RCSB], [http://www.ebi.ac.uk/pdbsum/2q4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Y1926_ARATH Y1926_ARATH]] May play a role in the intracellular transport of hydrophobic ligands (Potential). | + | [https://www.uniprot.org/uniprot/NB_ARATH NB_ARATH] Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively) (PubMed:32295384). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo (PubMed:32295384, PubMed:19938152).<ref>PMID:19938152</ref> <ref>PMID:32295384</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Structural genomic]] | + | [[Category: Large Structures]] |
| - | [[Category: Kondrashov, D A]] | + | [[Category: Kondrashov DA]] |
| - | [[Category: Levin, E J]] | + | [[Category: Levin EJ]] |
| - | [[Category: Phillips, G N]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Wesenberg, G E]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: At1g79260]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
NB_ARATH Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively) (PubMed:32295384). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo (PubMed:32295384, PubMed:19938152).[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bianchetti CM, Blouin GC, Bitto E, Olson JS, Phillips GN Jr. The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1. Proteins. 2010 Mar;78(4):917-31. PMID:19938152 doi:10.1002/prot.22617
- ↑ De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and human nitrobindins: structure and function. Antioxid Redox Signal. 2020 Apr 16. doi: 10.1089/ars.2019.7874. PMID:32295384 doi:http://dx.doi.org/10.1089/ars.2019.7874
- ↑ 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
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