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| - | [[Image:1sk5.gif|left|200px]] | |
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| - | {{Structure
| + | ==The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition== |
| - | |PDB= 1sk5 |SIZE=350|CAPTION= <scene name='initialview01'>1sk5</scene>, resolution 0.89Å
| + | <StructureSection load='1sk5' size='340' side='right'caption='[[1sk5]], [[Resolution|resolution]] 0.89Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.89Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sk5 OCA], [http://www.ebi.ac.uk/pdbsum/1sk5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1sk5 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition'''
| + | [[Category: Dickerson RE]] |
| - | | + | [[Category: Han GW]] |
| - | | + | [[Category: Kopka ML]] |
| - | ==Overview==
| + | [[Category: Langs D]] |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1SK5 is a [[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=1SK5 OCA].
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| - | | + | |
| - | ==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://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Dickerson, R E.]] | + | |
| - | [[Category: Han, G W.]] | + | |
| - | [[Category: Kopka, M L.]] | + | |
| - | [[Category: Langs, D.]] | + | |
| - | [[Category: dna/dna double helix]]
| + | |
| - | [[Category: popypurine tract sequence of hiv-1]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:43:09 2008''
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