1sk5: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1sk5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SK5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1sk5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SK5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.89&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sk5 OCA], [https://pdbe.org/1sk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1sk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sk5 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sk5 OCA], [https://pdbe.org/1sk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1sk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sk5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:11173466</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1sk5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Dickerson, R E]]
[[Category: Dickerson RE]]
[[Category: Han, G W]]
[[Category: Han GW]]
[[Category: Kopka, M L]]
[[Category: Kopka ML]]
[[Category: Langs, D]]
[[Category: Langs D]]
[[Category: Dna]]
[[Category: Dna/dna double helix]]
[[Category: Popypurine tract sequence of hiv-1]]

Latest revision as of 00:36, 29 June 2023

The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognitionThe ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition

Structural highlights

1sk5 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.89Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1sk5, resolution 0.89Å

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