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| - | [[Image:348d.gif|left|200px]] | |
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| - | {{Structure
| + | ==X-RAY CRYSTAL STRUCTURES OF THE DECAMER DGACCGCGGTC: LOW SALT CONCENTRATION== |
| - | |PDB= 348d |SIZE=350|CAPTION= <scene name='initialview01'>348d</scene>, resolution 1.700Å
| + | <StructureSection load='348d' size='340' side='right'caption='[[348d]], [[Resolution|resolution]] 1.70Å' 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'>[[348d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=348D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=348D 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]] 1.7Å</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=348d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=348d OCA], [https://pdbe.org/348d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=348d RCSB], [https://www.ebi.ac.uk/pdbsum/348d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=348d ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=348d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=348d OCA], [http://www.ebi.ac.uk/pdbsum/348d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=348d RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Finley JB]] |
| - | '''X-RAY CRYSTAL STRUCTURES OF THE DECAMER DGACCGCGGTC: LOW SALT CONCENTRATION'''
| + | [[Category: Luo M]] |
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| - | | + | |
| - | ==Overview==
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| - | The X-ray crystal structure of the DNA decamer d(GACCGCGGTC), containing half the human papilloma virus E2 binding site, has been solved from two crystals grown at different ionic conditions (50 mM MgCl2and 50 mM spermine or 1.56 mM MgCl2and 1.56 mM spermine). Despite the variation in salt concentration, the two DNA structures are in a very similar, A-type DNA conformation, with helical axes curving towards the major groove. Although the salt concentrations do not effect the helical parameters or hydration to a large degree, there is a change in the overall helical curvature; 18 degrees and 31 degrees for the low and high salt structures, respectively. This curvature appears to be sequence specific and biologically relevant when compared with similar DNA structures, including the E2 binding site of a protein-DNA complex.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 348D 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=348D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGGTC)., Finley JB, Luo M, Nucleic Acids Res. 1998 Dec 15;26(24):5719-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9838004 9838004]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Finley, J B.]] | + | |
| - | [[Category: Luo, M.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:36 2008''
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