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1da3

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[[Image:1da3.gif|left|200px]]
 
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{{Structure
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==THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN==
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|PDB= 1da3 |SIZE=350|CAPTION= <scene name='initialview01'>1da3</scene>, resolution 2.000&Aring;
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<StructureSection load='1da3' size='340' side='right'caption='[[1da3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5&#39;-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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<table><tr><td colspan='2'>[[1da3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DA3 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [https://pdbe.org/1da3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB], [https://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1da3 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1da3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1da3 OCA], [http://www.ebi.ac.uk/pdbsum/1da3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1da3 RCSB]</span>
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__TOC__
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}}
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</StructureSection>
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[[Category: Large Structures]]
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'''THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN'''
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[[Category: Baikalov I]]
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[[Category: Dickerson RE]]
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[[Category: Grzeskowiak K]]
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==Overview==
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[[Category: Quintana J]]
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The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees, imply ten base-pairs or one complete decamer double helix per asymmetric unit. The 2282 two-sigma data to 2.0 A refine to R = 17.2% with 45 water molecules, 1.5 hexavalent hydrated magnesium complexes, and 0.5 chloride ion per asymmetric unit. Neighboring helices interlock backbone chains and major grooves, crossing at an angle of 120 degrees in a manner that yields an excellent model for a Holliday junction. Local helix parameters differ markedly in the trigonal and orthorhombic structures, with the trigonal helix exhibiting behavior closer to that expected of B-DNA in solution. The trigonal form has an average of 10.6 base-pairs per turn, in contrast to 9.7 base-pairs per turn in the orthorhombic cell. A comparison of all known B-DNA decamer and dodecamer crystal structure analyses indicates that, the greater the cell volume per base-pair (and hence the more open the crystal structure), the closer the mean helix twist approaches an expected 10.6 base-pairs per turn.
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[[Category: Yanagi K]]
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==About this Structure==
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1DA3 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=1DA3 OCA].
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==Reference==
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The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn., Baikalov I, Grzeskowiak K, Yanagi K, Quintana J, Dickerson RE, J Mol Biol. 1993 Jun 5;231(3):768-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8515450 8515450]
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[[Category: Protein complex]]
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[[Category: Baikalov, I.]]
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[[Category: Dickerson, R E.]]
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[[Category: Grzeskowiak, K.]]
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[[Category: Quintana, J.]]
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[[Category: Yanagi, K.]]
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[[Category: b-dna]]
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[[Category: double helix]]
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[[Category: modified]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:37:34 2008''
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Current revision

THE CRYSTAL STRUCTURE OF THE TRIGONAL DECAMER C-G-A-T-C-G-6MEA-T-C-G: A B-DNA HELIX WITH 10.6 BASE-PAIRS PER TURN

PDB ID 1da3

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