2npz: Difference between revisions

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{{Seed}}
[[Image:2npz.png|left|200px]]


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==Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker==
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<StructureSection load='2npz' size='340' side='right'caption='[[2npz]], [[Resolution|resolution]] 3.35&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'>[[2npz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NPZ 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]] 3.35&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=PDI:PHOSPHORIC+ACID+MONO-(3-HYDROXY-PROPYL)+ESTER'>PDI</scene></td></tr>
{{STRUCTURE_2npz|  PDB=2npz  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2npz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2npz OCA], [https://pdbe.org/2npz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2npz RCSB], [https://www.ebi.ac.uk/pdbsum/2npz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2npz ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.


===Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker===
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.,MacElrevey C, Spitale RC, Krucinska J, Wedekind JE Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25. Epub 2007, Jun 15. PMID:17582172<ref>PMID:17582172</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2npz" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17582172}}, adds the Publication Abstract to the page
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17582172 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_17582172}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NPZ OCA].
[[Category: Krucinska J]]
 
[[Category: MacElrevey C]]
==Reference==
[[Category: Wedekind JE]]
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme., MacElrevey C, Spitale RC, Krucinska J, Wedekind JE, Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25. Epub 2007, Jun 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17582172 17582172]
[[Category: Krucinska, J.]]
[[Category: MacElrevey, C.]]
[[Category: Wedekind, J E.]]
[[Category: E loop]]
[[Category: Hairpin]]
[[Category: Propyl]]
[[Category: Ribozyme]]
[[Category: Rna]]
[[Category: S turn]]
 
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