2q42

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2q42" [edit=sysop:move=sysop])
Current revision (11:18, 30 August 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2q42.png|left|200px]]
 
-
<!--
+
==Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350==
-
The line below this paragraph, containing "STRUCTURE_2q42", creates the "Structure Box" on the page.
+
<StructureSection load='2q42' size='340' side='right'caption='[[2q42]], [[Resolution|resolution]] 1.74&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'>[[2q42]] is a 2 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=2Q42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q42 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]] 1.742&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_2q42| PDB=2q42 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q42 OCA], [https://pdbe.org/2q42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q42 RCSB], [https://www.ebi.ac.uk/pdbsum/2q42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q42 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GLO2N_ARATH GLO2N_ARATH] Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid.<ref>PMID:16227621</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/q4/2q42_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=2q42 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 glyoxalase II from Arabidopsis thaliana gene At2g31350===
+
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 2q42" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page
+
*[[Glyoxalase 3D structures|Glyoxalase 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==
+
-
[[2q42]] is a 2 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=2Q42 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:017850744</ref><references group="xtra"/>
+
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Hydroxyacylglutathione hydrolase]]
+
[[Category: Large Structures]]
-
[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
+
[[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: At2g31350]]
+
-
[[Category: B-lactamase fold]]
+
-
[[Category: Center for eukaryotic structural genomic]]
+
-
[[Category: Cesg]]
+
-
[[Category: Ensemble refinement]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metallo-hydrolase]]
+
-
[[Category: Mitochondrial isozyme]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi]]
+
-
[[Category: Refinement methodology development]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Thioester hydrolase]]
+
-
[[Category: Zinc/iron binuclear center]]
+

Current revision

Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350

PDB ID 2q42

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/2q42"
Personal tools