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| <!--
| | ==THE STRUCTURE OF A B-DNA DECAMER WITH A CENTRAL T-A STEP: C-G-A-T-T-A-A-T-C-G== |
| The line below this paragraph, containing "STRUCTURE_1d49", creates the "Structure Box" on the page.
| | <StructureSection load='1d49' size='340' side='right'caption='[[1d49]], [[Resolution|resolution]] 1.50Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[1d49]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D49 FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
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| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| {{STRUCTURE_1d49| PDB=1d49 | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d49 OCA], [https://pdbe.org/1d49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d49 RCSB], [https://www.ebi.ac.uk/pdbsum/1d49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d49 ProSAT]</span></td></tr> |
| | | </table> |
| '''THE STRUCTURE OF A B-DNA DECAMER WITH A CENTRAL T-A STEP: C-G-A-T-T-A-A-T-C-G'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Dickerson RE]] |
| The X-ray crystal structure analysis of the decamer C-G-A-T-T-A-A-T-C-G has been carried out to a resolution of 1.5 A. The crystals are space group P2(1)2(1)2(1), cell dimensions a = 38.60 A, b = 39.10 A, c = 33.07 A. The structure was solved by molecular replacement and refined with X-PLOR and NUCLSQ. The final R factor for a model with 404 DNA atoms, 108 water molecules and one magnesium hexahydrate cation is 15.7%. The double helix is essentially isostructural with C-G-A-T-C-G-A-T-C-G, with closely similar local helix parameters. The structure of the T-T-A-A center differs from that found in C-G-C-G-T-T-A-A-C-G-C-G in that the minor groove in our decamer is wide at the central T-A step rather than narrow, and the twist angle of the T-A step is small (31.1 degrees) rather than large. Whereas the tetrad model provides a convenient framework for discussing local DNA helix structure, it cannot be the entire story. The articulated helix model of DNA structure proposes that certain sequence regions of DNA show preferential twisting or bending properties, whereas other regions are less capable of deformation, in a manner that may be useful in sequence recognition by drugs and protein. Further crystal structure analyses should help to delineate the precise nature of sequence-dependent articulation in the DNA double helix.
| | [[Category: Grzeskowiak K]] |
| | | [[Category: Quintana JR]] |
| ==About this Structure==
| | [[Category: Yanagi K]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D49 OCA]. | |
| | |
| ==Reference== | |
| Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G., Quintana JR, Grzeskowiak K, Yanagi K, Dickerson RE, J Mol Biol. 1992 May 20;225(2):379-95. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1593626 1593626]
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| [[Category: Dickerson, R E.]]
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| [[Category: Grzeskowiak, K.]] | |
| [[Category: Quintana, J R.]] | |
| [[Category: Yanagi, K.]] | |
| [[Category: B-dna]] | |
| [[Category: Double helix]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:26:04 2008''
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