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1bd1
From Proteopedia
(New page: 200px<br /><applet load="1bd1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bd1, resolution 1.600Å" /> '''CRYSTALLOGRAPHIC ST...) |
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| - | [[Image:1bd1.gif|left|200px]]<br /><applet load="1bd1" size=" | + | [[Image:1bd1.gif|left|200px]]<br /><applet load="1bd1" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1bd1, resolution 1.600Å" /> | caption="1bd1, resolution 1.600Å" /> | ||
'''CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA'''<br /> | '''CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. | + | The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA. |
==About this Structure== | ==About this Structure== | ||
| - | 1BD1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with TEA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1BD1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TEA:'>TEA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BD1 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:53:57 2008'' |
Revision as of 09:54, 21 February 2008
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CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA
Overview
The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA.
About this Structure
1BD1 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystallographic study of one turn of G/C-rich B-DNA., Heinemann U, Alings C, J Mol Biol. 1989 Nov 20;210(2):369-81. PMID:2600970
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