1d23: Difference between revisions

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[[Image:1d23.gif|left|200px]]


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==THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS==
The line below this paragraph, containing "STRUCTURE_1d23", creates the "Structure Box" on the page.
<StructureSection load='1d23' size='340' side='right'caption='[[1d23]], [[Resolution|resolution]] 1.50&Aring;' 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'>[[1d23]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D23 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D23 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]] 1.5&#8491;</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_1d23|  PDB=1d23  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d23 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d23 OCA], [https://pdbe.org/1d23 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d23 RCSB], [https://www.ebi.ac.uk/pdbsum/1d23 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d23 ProSAT]</span></td></tr>
 
</table>
'''THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Dickerson RE]]
The crystal structure of the DNA decamer C-G-A-T-C-G-A-T-C-G has been solved to a resolution of 1.5 A, with a final R-factor of 16.1% for 5,107 two-sigma reflections. Crystals are orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 38.93 A, b = 39.63 A, c = 33.30 A, and 10 base pairs/asymmetric unit. The final structure contains 404 DNA atoms, 142 water molecules treated as oxygen atoms, and two Mg(H2O)6(2+) complexes. Decamers stack atop one another to simulate continuous helical columns through the crystal, as with three previously solved monoclinic decamers, but the lateral contacts between columns are quite different in the orthorhombic and monoclinic cells. Narrow and wide regions of the minor groove exhibit a single spine or two ribbons of hydration, respectively, and the minor groove is widest when BII phosphate conformations are opposed diagonally across the groove. Phosphate conformation, in turn, appears to have a base sequence dependence. Twist, rise, cup, and roll are linked as has been observed in the three monoclinic decamers and can be characterized by high or low twist profiles. In all five known decamer crystal structures and eight representative dodecamers, a high twist profile is observed with G-C and G-A steps whereas all other R-R steps are low twist profiles (R = purine). A-T and A-C steps are intermediate in character whereas C-A and C-G exhibit behavior that is strongly influenced by the profiles of the preceding and following steps. When sufficient data are in hand, sequence/structure relationships for all helix parameters probably should be considered in a 4-base pair context. At this stage of limited information the problem is compounded because there are 136 unique 4-base steps x-A-B-y in a double helix as compared with only 10 2-base steps A-B.
[[Category: Grzeskowiak K]]
 
[[Category: Prive GG]]
==About this Structure==
[[Category: Yanagi K]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D23 OCA].  
 
==Reference==
The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals., Grzeskowiak K, Yanagi K, Prive GG, Dickerson RE, J Biol Chem. 1991 May 15;266(14):8861-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2026600 2026600]
[[Category: Dickerson, R E.]]
[[Category: Grzeskowiak, K.]]
[[Category: Prive, G G.]]
[[Category: Yanagi, K.]]
[[Category: B-dna]]
[[Category: Double helix]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:21:50 2008''

Latest revision as of 09:48, 7 February 2024

THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALSTHE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALS

Structural highlights

1d23 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d23, resolution 1.50Å

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