1d13

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[[Image:1d13.gif|left|200px]]
 
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==MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)==
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The line below this paragraph, containing "STRUCTURE_1d13", creates the "Structure Box" on the page.
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<StructureSection load='1d13' size='340' side='right'caption='[[1d13]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1d13]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D13 FirstGlance]. <br>
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</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&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d13 OCA], [https://pdbe.org/1d13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d13 RCSB], [https://www.ebi.ac.uk/pdbsum/1d13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d13 ProSAT]</span></td></tr>
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{{STRUCTURE_1d13| PDB=1d13 | SCENE= }}
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</table>
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__TOC__
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'''MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)'''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Coll M]]
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==Overview==
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[[Category: Frederick CA]]
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The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.
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[[Category: Quigley GJ]]
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[[Category: Rich A]]
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==About this Structure==
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[[Category: Teng M-K]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D13 OCA].
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[[Category: Van Boom JH]]
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[[Category: Van Der Marel GA]]
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==Reference==
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[[Category: Wang AH-J]]
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Molecular structure of an A-DNA decamer d(ACCGGCCGGT)., Frederick CA, Quigley GJ, Teng MK, Coll M, Van der Marel GA, Van Boom JH, Rich A, Wang AH, Eur J Biochem. 1989 May 1;181(2):295-307. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2714286 2714286]
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[[Category: Boom, J H.Van.]]
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[[Category: Coll, M.]]
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[[Category: Frederick, C A.]]
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[[Category: Marel, G A.Van Der.]]
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[[Category: Quigley, G J.]]
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[[Category: Rich, A.]]
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[[Category: Teng, M K.]]
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[[Category: Wang, A H.J.]]
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[[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 Fri May 2 13:19:54 2008''
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Current revision

MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)

PDB ID 1d13

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