1g4q
From Proteopedia
(New page: 200px<br /> <applet load="1g4q" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g4q, resolution 1.15Å" /> '''RNA/DNA HYBRID DECA...) |
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| - | [[Image:1g4q.gif|left|200px]]<br /> | + | [[Image:1g4q.gif|left|200px]]<br /><applet load="1g4q" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="1g4q" size=" | + | |
caption="1g4q, resolution 1.15Å" /> | caption="1g4q, resolution 1.15Å" /> | ||
'''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG'''<br /> | '''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG'''<br /> | ||
==Overview== | ==Overview== | ||
| - | For the first time, ab initio direct methods have been used to solve the | + | For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure. |
==About this Structure== | ==About this Structure== | ||
| - | 1G4Q is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1G4Q is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. |
==Reference== | ==Reference== | ||
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11173466 11173466] | Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11173466 11173466] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Han, G | + | [[Category: Han, G W.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: MPD]] | [[Category: MPD]] | ||
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[[Category: rna/dna hybrid]] | [[Category: rna/dna hybrid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:46:06 2008'' |
Revision as of 10:46, 21 February 2008
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RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG
Overview
For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.
About this Structure
1G4Q is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466
Page seeded by OCA on Thu Feb 21 12:46:06 2008
