1g4q: Difference between revisions

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New page: left|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 />
<applet load="1g4q" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1g4q, resolution 1.15&Aring;" />
'''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG'''<br />


==Overview==
==RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG==
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.
<StructureSection load='1g4q' size='340' side='right'caption='[[1g4q]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1g4q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G4Q FirstGlance]. <br>
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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#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>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [https://pdbe.org/1g4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB], [https://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g4q ProSAT]</span></td></tr>
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]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Han, G.W.]]
</StructureSection>
[[Category: CA]]
[[Category: Large Structures]]
[[Category: MPD]]
[[Category: Han GW]]
[[Category: direct methods]]
[[Category: polypurine tract of hiv-1]]
[[Category: rna/dna hybrid]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 14:03:53 2007''

Latest revision as of 07:22, 7 February 2024

RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG

1g4q, resolution 1.15Å

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