1d28: Difference between revisions
New page: left|200px<br /><applet load="1d28" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d28, resolution 2.700Å" /> '''CRYSTAL AND MOLECUL... |
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[[Image:1d28.gif|left|200px]]<br /><applet load="1d28" size=" | [[Image:1d28.gif|left|200px]]<br /><applet load="1d28" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1d28, resolution 2.700Å" /> | caption="1d28, resolution 2.700Å" /> | ||
'''CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG)'''<br /> | '''CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG)'''<br /> | ||
==Overview== | ==Overview== | ||
The crystal structure of the dodecanucleotide d(CGTGAATTCACG) has been | The crystal structure of the dodecanucleotide d(CGTGAATTCACG) has been determined to a resolution of 2.7 A and refined to an R factor of 17.0% for 1532 reflections. The sequence crystallizes as a B-form double helix, with Watson-Crick base pairing. This sequence contains the EcoRI restriction endonuclease recognition site, GAATTC, and is flanked by CGT on the 5'-end and ACG on the 3'-end, in contrast to the CGC on the 5'-end and GCG on the 3'-end in the parent dodecamer d(CGCGAATTCGCG). A comparison with the isomorphous parent compound shows that any changes in the structure induced by the change in the sequence in the flanking region are highly localized. The global conformation of the duplex is conserved. The overall bend in the helix is 10 degrees. The average helical twist values for the present and the parent structures are 36.5 degrees and 36.4 degrees, respectively, corresponding to 10 base pairs per turn. The buckle at the substituted sites are significantly different from those seen at the corresponding positions in the parent dodecamer. Step 2 (GpT) is underwound with respect to the parent structure (27 degrees vs 36 degrees) and step 3 (TpG) is overwound (34 degrees vs 27 degrees). There is a spine of hydration in the narrow minor groove. The N3 atom of adenine on the substituted A10 and A22 bases are involved in the formation of hydrogen bonds with other duplexes or with water; the N3 atom of guanine on G10 and G22 bases in the parent structure does not form hydrogen bonds. | ||
==About this Structure== | ==About this Structure== | ||
1D28 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:// | 1D28 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=1D28 OCA]. | ||
==Reference== | ==Reference== | ||
Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG)., Narayana N, Ginell SL, Russu IM, Berman HM, Biochemistry. 1991 May 7;30(18):4449-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2021634 2021634] | Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG)., Narayana N, Ginell SL, Russu IM, Berman HM, Biochemistry. 1991 May 7;30(18):4449-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2021634 2021634] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Berman, H | [[Category: Berman, H M.]] | ||
[[Category: Ginell, S | [[Category: Ginell, S L.]] | ||
[[Category: Narayana, N.]] | [[Category: Narayana, N.]] | ||
[[Category: Russu, I | [[Category: Russu, I M.]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:09 2008'' | ||
Revision as of 13:12, 21 February 2008
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CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG)
OverviewOverview
The crystal structure of the dodecanucleotide d(CGTGAATTCACG) has been determined to a resolution of 2.7 A and refined to an R factor of 17.0% for 1532 reflections. The sequence crystallizes as a B-form double helix, with Watson-Crick base pairing. This sequence contains the EcoRI restriction endonuclease recognition site, GAATTC, and is flanked by CGT on the 5'-end and ACG on the 3'-end, in contrast to the CGC on the 5'-end and GCG on the 3'-end in the parent dodecamer d(CGCGAATTCGCG). A comparison with the isomorphous parent compound shows that any changes in the structure induced by the change in the sequence in the flanking region are highly localized. The global conformation of the duplex is conserved. The overall bend in the helix is 10 degrees. The average helical twist values for the present and the parent structures are 36.5 degrees and 36.4 degrees, respectively, corresponding to 10 base pairs per turn. The buckle at the substituted sites are significantly different from those seen at the corresponding positions in the parent dodecamer. Step 2 (GpT) is underwound with respect to the parent structure (27 degrees vs 36 degrees) and step 3 (TpG) is overwound (34 degrees vs 27 degrees). There is a spine of hydration in the narrow minor groove. The N3 atom of adenine on the substituted A10 and A22 bases are involved in the formation of hydrogen bonds with other duplexes or with water; the N3 atom of guanine on G10 and G22 bases in the parent structure does not form hydrogen bonds.
About this StructureAbout this Structure
1D28 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG)., Narayana N, Ginell SL, Russu IM, Berman HM, Biochemistry. 1991 May 7;30(18):4449-55. PMID:2021634
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