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218d

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[[Image:218d.gif|left|200px]]
 
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==THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS==
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The line below this paragraph, containing "STRUCTURE_218d", creates the "Structure Box" on the page.
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<StructureSection load='218d' size='340' side='right'caption='[[218d]], [[Resolution|resolution]] 2.25&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'>[[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>
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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]] 2.25&#8491;</td></tr>
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<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>
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{{STRUCTURE_218d| PDB=218d | SCENE= }}
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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=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>
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</table>
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'''THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Berman HM]]
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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.
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[[Category: Eaton MD]]
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[[Category: Gaffney B]]
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==About this Structure==
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[[Category: Jones R]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=218D OCA].
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[[Category: Vojtechovsky J]]
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/8527436 8527436]
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[[Category: Berman, H M.]]
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[[Category: Eaton, M D.]]
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[[Category: Gaffney, B.]]
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[[Category: Jones, R.]]
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[[Category: Vojtechovsky, J.]]
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[[Category: B-dna]]
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[[Category: Double helix]]
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[[Category: Mismatched]]
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[[Category: Modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:19:17 2008''
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Current revision

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

PDB ID 218d

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