2q4n

From Proteopedia

(Difference between revisions)

Current revision

Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260

Structural highlights

2q4n is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.32Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q4n"

@@ Line 1: / Line 1: @@
 ==Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260==
-<StructureSection load='2q4n' size='340' side='right' caption='[[2q4n]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
+<StructureSection load='2q4n' size='340' side='right'caption='[[2q4n]], [[Resolution|resolution]] 1.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q4n]] is a 1 chain structure with 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=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]] 1.32&#8491;</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 Arabidopsis thaliana])</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://www.rcsb.org/pdb/explore.do?structureId=2q4n RCSB], [http://www.ebi.ac.uk/pdbsum/2q4n PDBsum]</span></td></tr>
 </table>
+== Function ==
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4n_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4n_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q4n ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2q4n" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 31: / Line 34: @@
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
+[[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: Center for eukaryotic structural genomic]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Refinement methodology development]]
-[[Category: Structural genomic]]
-[[Category: Unknown function]]

2q4n

From Proteopedia

Current revision

Ensemble refinement of the crystal structure of protein from Arabidopsis thaliana At1g79260

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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