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| - | [[Image:1vj4.gif|left|200px]] | |
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| - | {{Structure
| + | ==SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)== |
| - | |PDB= 1vj4 |SIZE=350|CAPTION= <scene name='initialview01'>1vj4</scene>, resolution 1.800Å
| + | <StructureSection load='1vj4' size='340' side='right'caption='[[1vj4]], [[Resolution|resolution]] 1.80Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <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'>[[1vj4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJ4 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]] 1.8Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vj4 OCA], [https://pdbe.org/1vj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1vj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vj4 ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vj4 OCA], [http://www.ebi.ac.uk/pdbsum/1vj4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vj4 RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Cruse WB]] |
| - | '''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)'''
| + | [[Category: Kennard O]] |
| - | | + | [[Category: Rabinovich D]] |
| - | | + | [[Category: Salisbury SA]] |
| - | ==Overview==
| + | [[Category: Shakked Z]] |
| - | The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.
| + | [[Category: Viswamitra MA]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1VJ4 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=1VJ4 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6854642 6854642]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Cruse, W B.]] | + | |
| - | [[Category: Kennard, O.]] | + | |
| - | [[Category: Rabinovich, D.]] | + | |
| - | [[Category: Salisbury, S A.]] | + | |
| - | [[Category: Shakked, Z.]] | + | |
| - | [[Category: Viswamitra, M A.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:25:15 2008''
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