2q3r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2q3r" [edit=sysop:move=sysop])
Current revision (11:17, 30 August 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2q3r.png|left|200px]]
 
-
<!--
+
==Ensemble refinement of the protein crystal structure of At1g76680 from Arabidopsis thaliana==
-
The line below this paragraph, containing "STRUCTURE_2q3r", creates the "Structure Box" on the page.
+
<StructureSection load='2q3r' size='340' side='right'caption='[[2q3r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2q3r]] 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=2Q3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3R FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-
{{STRUCTURE_2q3r| PDB=2q3r | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3r OCA], [https://pdbe.org/2q3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3r RCSB], [https://www.ebi.ac.uk/pdbsum/2q3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3r ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/OPR1_ARATH OPR1_ARATH] Specifically cleaves olefinic bonds in alpha,beta-unsaturated carbonyls and may be involved in detoxification or modification of these reactive compounds. May be involved in the biosynthesis or metabolism of oxylipin signaling molecules. In vitro, reduces 9R,13R-12-oxophyodienoic acid (9R,13R-OPDA) to 9R,13R-OPC-8:0, but only poorly 9S,13S-OPDA, the natural precursor of jasmonic acid. Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro and in vivo by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT).<ref>PMID:19605548</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/q3/2q3r_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/main_output.php?pdb_ID=2q3r ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 the protein crystal structure of At1g76680 from Arabidopsis thaliana===
+
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<ref>PMID:17850744</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2q3r" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
+
*[[12-oxophytodienoate reductase 3D structures|12-oxophytodienoate reductase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 17850744 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17850744}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[2q3r]] 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=2Q3R OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:017850744</ref><references group="xtra"/>
+
-
[[Category: 12-oxophytodienoate reductase]]
+
[[Category: Arabidopsis thaliana]]
[[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: Center for eukaryotic structural genomic]]
+
-
[[Category: Cesg]]
+
-
[[Category: Ensemble refinement]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi]]
+
-
[[Category: Refinement methodology development]]
+
-
[[Category: Structural genomic]]
+

Current revision

Ensemble refinement of the protein crystal structure of At1g76680 from Arabidopsis thaliana

PDB ID 2q3r

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q3r"
Personal tools