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| [[Image:160d.gif|left|200px]]
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| {{Structure
| | ==HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS== |
| |PDB= 160d |SIZE=350|CAPTION= <scene name='initialview01'>160d</scene>, resolution 1.650Å
| | <StructureSection load='160d' size='340' side='right'caption='[[160d]], [[Resolution|resolution]] 1.65Å' scene=''> |
| |SITE=
| | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>
| | <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> |
| |ACTIVITY=
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</td></tr> |
| |GENE=
| | <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> |
| |DOMAIN=
| | </table> |
| |RELATEDENTRY=
| | __TOC__ |
| |RESOURCES=<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://www.ebi.ac.uk/pdbsum/160d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=160d RCSB]</span>
| | </StructureSection> |
| }}
| | [[Category: Large Structures]] |
| | | [[Category: Ramakrishnan B]] |
| '''HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS'''
| | [[Category: Sundaralingam M]] |
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| ==Overview==
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| 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.
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| ==About this Structure==
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| 160D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=160D OCA].
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| ==Reference==
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| 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:[http://www.ncbi.nlm.nih.gov/pubmed/8510155 8510155]
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| [[Category: Protein complex]] | |
| [[Category: Ramakrishnan, B.]] | |
| [[Category: Sundaralingam, M.]] | |
| [[Category: a-dna]]
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| [[Category: double helix]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:28:38 2008''
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