View source for 4opk


==Bh-RNaseH:2'-SMe-DNA complex==
<StructureSection load='4opk' size='340' side='right'caption='[[4opk]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4opk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OPK 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]] 1.539&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</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=4opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4opk OCA], [https://pdbe.org/4opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4opk RCSB], [https://www.ebi.ac.uk/pdbsum/4opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4opk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The DNA dodecamer 5'-d(CGCGAATTCGCG)-3' is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2'-deoxynucleotide structures determined over the last 30 years. The dodecamer has commonly served as a template to analyze the effects of sequence on DNA conformation, the conformational properties of chemically modified nucleotides, DNA-ligand interactions as well as water structure and DNA-cation binding. Although molecular replacement is the phasing method of choice given the large number of available models of the dodecamer, this strategy often fails as a result of conformational changes caused by chemical modification, mismatch pairs, or differing packing modes. Here, we describe an alternative approach to determine crystal structures of the dodecamer in cases where molecular replacement does not produce a solution or when crystals of the DNA alone cannot be grown. It is based on the discovery that many dodecamers of the above sequence can be readily co-crystallized with Bacillus halodurans RNase H, whereby the enzyme is unable to cleave the DNA. Determination of the structure of the complex using the protein portion as the search model yields a structural model of the DNA. Provided crystals of the DNA alone are also available, the DNA model from the complex then enables phasing their structures by molecular replacement.

Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes.,Egli M, Pallan PS Methods Mol Biol. 2016;1320:111-26. doi: 10.1007/978-1-4939-2763-0_8. PMID:26227040<ref>PMID:26227040</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4opk" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Alkalihalobacillus halodurans]]
[[Category: Large Structures]]
[[Category: Egli M]]
[[Category: Pallan PS]]