192d
From Proteopedia
(New page: 200px<br /><applet load="192d" size="450" color="white" frame="true" align="right" spinBox="true" caption="192d, resolution 1.920Å" /> '''RECOMBINATION-LIKE ...) |
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| - | [[Image:192d.gif|left|200px]]<br /><applet load="192d" size=" | + | [[Image:192d.gif|left|200px]]<br /><applet load="192d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="192d, resolution 1.920Å" /> | caption="192d, resolution 1.920Å" /> | ||
'''RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)'''<br /> | '''RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have solved the single crystal X-ray structure of the synthetic DNA | + | We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules. |
==About this Structure== | ==About this Structure== | ||
| - | 192D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 192D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=192D OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Malinina, L.]] | [[Category: Malinina, L.]] | ||
[[Category: Salas, X.]] | [[Category: Salas, X.]] | ||
| - | [[Category: Subirana, J | + | [[Category: Subirana, J A.]] |
[[Category: Urpi, L.]] | [[Category: Urpi, L.]] | ||
[[Category: NA]] | [[Category: NA]] | ||
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[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:39:10 2008'' |
Revision as of 09:39, 21 February 2008
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RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)
Overview
We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.
About this Structure
192D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Recombination-like structure of d(CCGCGG)., Malinina L, Urpi L, Salas X, Huynh-Dinh T, Subirana JA, J Mol Biol. 1994 Oct 28;243(3):484-93. PMID:7966274
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