218d: Difference between revisions

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New page: left|200px<br /><applet load="218d" size="350" color="white" frame="true" align="right" spinBox="true" caption="218d, resolution 2.250Å" /> '''THE STRUCTURE OF A ...
 
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'''THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS'''<br />


==Overview==
==THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS==
The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been, determined to a resolution of 2.25 A and refined to a final R factor of, 16.7%. The volume of the unit cell is significantly smaller by 16% than, the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R., M., Takano, T., Broka, C., Tanaka, S., Itakura, K., &amp; Dickerson, R. E., (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is, in a different position in the unit cell, rotated by -85.9 degrees, and, translated by 9.9 A around the helical axis with respect to the parent, structure. The intermolecular arrangement of helices, characterized by, double hydrogen bonded guanine-guanine minor groove interactions, remains, conserved. The molecular geometry exhibits several significant changes, that are related to the changed position of the helix and the presence of, two mismatched base pairs with O6-methylguanine. Both mispairs are found, in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups, are in proximal orientation. The hydration pattern of the structure is, different and can be related to changes in the minor groove geometry. An, incorrect model that was isomorphous to the parent dodecamer could be, refined to a low R factor. Characteristics of the refinement and of the, geometry that are indicative of incorrect structures have been analyzed.
<StructureSection load='218d' size='340' side='right'caption='[[218d]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[218d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=218D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=218D FirstGlance]. <br>
218D is a [http://en.wikipedia.org/wiki/Protein_complex 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=218D OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=218d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=218d OCA], [https://pdbe.org/218d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=218d RCSB], [https://www.ebi.ac.uk/pdbsum/218d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=218d ProSAT]</span></td></tr>
Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs., Vojtechovsky J, Eaton MD, Gaffney B, Jones R, Berman HM, Biochemistry. 1995 Dec 26;34(51):16632-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8527436 8527436]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Berman, H.M.]]
</StructureSection>
[[Category: Eaton, M.D.]]
[[Category: Large Structures]]
[[Category: Gaffney, B.]]
[[Category: Berman HM]]
[[Category: Jones, R.]]
[[Category: Eaton MD]]
[[Category: Vojtechovsky, J.]]
[[Category: Gaffney B]]
[[Category: b-dna]]
[[Category: Jones R]]
[[Category: double helix]]
[[Category: Vojtechovsky J]]
[[Category: mismatched]]
[[Category: modified]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:47:33 2008''

Latest revision as of 12:08, 14 February 2024

THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRSTHE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS

Structural highlights

218d 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 2.25Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

218d, resolution 2.25Å

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