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==HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS==
==HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS==
<StructureSection load='160d' size='340' side='right' caption='[[160d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='160d' size='340' side='right'caption='[[160d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[160d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=160D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=160D FirstGlance]. <br>
<table><tr><td colspan='2'>[[160d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=160D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=160D FirstGlance]. <br>
</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=160d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=160d OCA], [http://pdbe.org/160d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=160d RCSB], [http://www.ebi.ac.uk/pdbsum/160d PDBsum]</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]] 1.65&#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=160d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=160d OCA], [https://pdbe.org/160d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=160d RCSB], [https://www.ebi.ac.uk/pdbsum/160d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=160d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in the asymmetric unit. The structure was solved by molecular replacement and refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related molecule results in distortion of the backbone bonds of the fifth residue G(5), P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their favored gauche- and gauche+ conformations, respectively. In this close encounter the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11)) triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove, causing a toll on the backbone conformation of the adjacent residue G(5). A similar triplet base-pairing interaction with somewhat weaker hydrogen bonds occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20), does not perturb the backgone alpha and gamma torsions of G(15). Both the novel base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17) base-pair jolts the global helical base-pair parameters, inclination, tilt, roll, tip, etc. quite markedly. Therefore a better description of the helix parameters is obtained by splitting the duplex and calculating the local helix axis for the top half consisting of the first three base-pairs, and the lower half consisting of the last six base-pairs, omitting the fourth base-pair. The two half duplexes are bent by only 10 degrees. This structure further demonstrates that crystal packing interactions, which can also be governed by base sequence, play a dominant role in determining DNA conformation.
High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets.,Ramakrishnan B, Sundaralingam M J Mol Biol. 1993 May 20;231(2):431-44. PMID:8510155<ref>PMID:8510155</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 160d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ramakrishnan, B]]
[[Category: Large Structures]]
[[Category: Sundaralingam, M]]
[[Category: Ramakrishnan B]]
[[Category: A-dna]]
[[Category: Sundaralingam M]]
[[Category: Dna]]
[[Category: Double helix]]

Latest revision as of 09:25, 7 February 2024

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETSHIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS

Structural highlights

160d 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 1.65Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

160d, resolution 1.65Å

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