1j9h

<StructureSection load='1j9h' size='340' side='right' caption='[[1j9h]], [[Resolution|resolution]] 1.40&Aring;' scene=''>

<table><tr><td colspan='2'>[[1j9h]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J9H FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9h OCA], [http://pdbe.org/1j9h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j9h RCSB], [http://www.ebi.ac.uk/pdbsum/1j9h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9h ProSAT]</span></td></tr>

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== Publication Abstract from PubMed ==

The crystal structure of a nonamer RNA duplex with a uridine bulge in each strand, r(gugucgcac)(2), was determined at 1.4 A resolution. The structure was solved by multiple anomalous diffraction phasing method using a three-wavelength data set collected at the Advanced Protein Source and refined to a final R(work)/R(free) of 21.2 %/23.4 % with 33,271 independent reflections (Friedel pairs unmerged). The RNA duplex crystallized in the tetragonal space group P4(1)22 with two independent molecules in the asymmetric unit. The unit cell dimensions are a=b=47.18 A and c=80.04 A. The helical region of the nonamer adopts the A-form conformation. The uridine bulges assume similar conformations, with uracils flipping out and protruding into the minor groove. The presence of the bulge induces very large twist angles (approximately +50 degrees) between the base-pairs flanking the bulges while causing profound kinks in the helix axis at the bulges. This severe twist and the large kink in turn produces a very narrow major groove at the middle of the molecule. The ribose sugars of the guanosines before the bulges adopt the C2'-endo conformation while the rest, including the bulges, are in the C3'-endo conformation. The intrastrand phosphate-phosphate (P-P) distance of the phosphate groups flanking the bulges (approximately 4.4 A) are significantly shorter than the average P-P distance in the duplex (6.0 A). This short distance between the two phosphate groups brings the non-bridging oxygen atoms close to each other where a calcium ion is bound to each strand. The calcium ions in molecule 1 are well defined while the calcium ions in molecule 2 are disordered.

Crystal structure of an RNA duplex r(gugucgcac)(2) with uridine bulges.,Xiong Y, Deng J, Sudarsanakumar C, Sundaralingam M J Mol Biol. 2001 Oct 26;313(3):573-82. PMID:11676540<ref>PMID:11676540</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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<div class="pdbe-citations 1j9h" style="background-color:#fffaf0;"></div>

== References ==

<references/>

[[Category: Deng, J]]

[[Category: Sudarsanakumar, C]]

[[Category: Sundaralingam, M]]

[[Category: Xiong, Y]]

[[Category: Uridine bulge]]