3qk4: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br>
</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We report the 2.6A resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4(3). This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.
The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2).,Venkadesh S, Mandal PK, Gautham N Biochem Biophys Res Commun. 2011 Apr 8;407(2):307-12. Epub 2011 Mar 21. PMID:21397589<ref>PMID:21397589</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qk4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gautham, N]]
[[Category: Gautham N]]
[[Category: Mandal, P K]]
[[Category: Mandal PK]]
[[Category: Venkadesh, S]]
[[Category: Venkadesh S]]
[[Category: A-dna duplex]]
[[Category: Dna]]

Latest revision as of 11:35, 20 March 2024

Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplexCrystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex

Structural highlights

3qk4 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3qk4, resolution 2.60Å

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OCA
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