2qvw: Difference between revisions

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New page: left|200px<br /><applet load="2qvw" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qvw, resolution 3.000Å" /> '''Structure of Giardi...
 
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[[Image:2qvw.jpg|left|200px]]<br /><applet load="2qvw" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2qvw, resolution 3.000&Aring;" />
'''Structure of Giardia Dicer refined against twinned data'''<br />


==Overview==
==Structure of Giardia Dicer refined against twinned data==
The crystal structure of the enzyme Dicer from Giardia intestinalis was, solved to 3.3 A resolution by MAD using crystals belonging to space group, P2(1)2(1)2 [Macrae et al. (2006), Science, 311, 195-198]. These crystals, were derived from crystals that diffracted X-rays to 3.0 A resolution but, were refractory to structure determination because they were twinned. It, is shown here that the original Dicer crystals represent an unusual case, of perfect pseudo-merohedral twinning of orthorhombic crystals. Before the, twinning problem was overcome, it was possible to calculate a, low-resolution electron-density map in space group P4(1) that was used to, build a partial molecular model. Experimental phases were sufficient to, identify heavy-atom sites that indicated space-group inconsistency, leading to identification of the true space group. This information guided, the search for different crystallization conditions that yielded untwinned, crystals and ultimately a fully interpretable electron-density map.
<StructureSection load='2qvw' size='340' side='right'caption='[[2qvw]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2qvw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVW FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=2qvw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvw OCA], [https://pdbe.org/2qvw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvw RCSB], [https://www.ebi.ac.uk/pdbsum/2qvw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DCL_GIAIC DCL_GIAIC] Involved in cleaving double-stranded RNA in the RNA interference (RNAi) pathway. It produces 21 to 23 bp dsRNAs (siRNAs) which target the selective destruction of homologous RNAs.<ref>PMID:16410517</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the enzyme Dicer from Giardia intestinalis was solved to 3.3 A resolution by MAD using crystals belonging to space group P2(1)2(1)2 [Macrae et al. (2006), Science, 311, 195-198]. These crystals were derived from crystals that diffracted X-rays to 3.0 A resolution but were refractory to structure determination because they were twinned. It is shown here that the original Dicer crystals represent an unusual case of perfect pseudo-merohedral twinning of orthorhombic crystals. Before the twinning problem was overcome, it was possible to calculate a low-resolution electron-density map in space group P4(1) that was used to build a partial molecular model. Experimental phases were sufficient to identify heavy-atom sites that indicated space-group inconsistency, leading to identification of the true space group. This information guided the search for different crystallization conditions that yielded untwinned crystals and ultimately a fully interpretable electron-density map.


==About this Structure==
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer.,MacRae IJ, Doudna JA Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):993-9. Epub 2007, Aug 17. PMID:17704568<ref>PMID:17704568</ref>
2QVW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVW OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer., Macrae IJ, Doudna JA, Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):993-9. Epub 2007, Aug 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17704568 17704568]
</div>
<div class="pdbe-citations 2qvw" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Giardia intestinalis]]
[[Category: Giardia intestinalis]]
[[Category: Ribonuclease III]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Doudna JA]]
[[Category: Doudna, J.A.]]
[[Category: MacRae IJ]]
[[Category: MacRae, I.J]]
[[Category: MN]]
[[Category: dicer]]
[[Category: hydrolase]]
[[Category: pseudo-merohedral twin]]
[[Category: rnai]]
 
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Latest revision as of 13:10, 26 July 2023

Structure of Giardia Dicer refined against twinned data

2qvw, resolution 3.00Å

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