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| - | [[Image:370d.gif|left|200px]] | |
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| - | {{Structure
| + | ==STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)== |
| - | |PDB= 370d |SIZE=350|CAPTION= <scene name='initialview01'>370d</scene>, resolution 1.670Å
| + | <StructureSection load='370d' size='340' side='right'caption='[[370d]], [[Resolution|resolution]] 1.67Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
| + | <table><tr><td colspan='2'>[[370d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=370D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=370D 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]] 1.67Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=370d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=370d OCA], [https://pdbe.org/370d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=370d RCSB], [https://www.ebi.ac.uk/pdbsum/370d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=370d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=370d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=370d OCA], [http://www.ebi.ac.uk/pdbsum/370d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=370d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)'''
| + | [[Category: Synthetic construct]] |
| - | | + | [[Category: Campos L]] |
| - | | + | [[Category: Fernandez LG]] |
| - | ==Overview==
| + | [[Category: Pyshnyi D]] |
| - | We have determined the structure of the synthetic DNA octamer d(pCpCpCpGpCpGpGpG) in five different crystal forms by single crystal X-ray diffraction. One crystal belongs to the space group P4(3)2(1)2 with a = b = 41.77, c = 25.15 A, whereas all others have the space group P2(1)2(1)2(1) with progressively decreasing unit cell volumes. In all crystals the octamer forms duplexes of A-DNA and all crystals display a similar packing mode, typical for A-DNA. The structure of the duplex varies from loose to very compact when going from one crystal form to another. The most compact form exhibits a volume of 995 A3 per base pair. Such a high density has never been found in A-DNA, being more characteristic of Z-DNA crystals. A comparison of the most with the least compact forms gives a RMS value of 1.7 A, with the distance between the phosphate centers through the major groove being almost twice shorter in the compact form. The phosphate-phosphate separation across the major groove in the compact form is extremely small, 0.7 A. The helical parameters also vary significantly in the various crystal forms. Differences in the helical twist can reach 13 degrees in the same step of the octamer in different crystal forms. The results prove that A-DNA is structurally very variable and demonstrate that the local structure of the same DNA fragment can strongly depend on the crystal environment.
| + | [[Category: Subirana JA]] |
| - | | + | [[Category: Verdaguer N]] |
| - | ==About this Structure==
| + | |
| - | 370D 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=370D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Structural variability of A-DNA in crystals of the octamer d(pCpCpCpGpCpGpGpG), Fernandez LG, Subirana JA, Verdaguer N, Pyshnyi D, Campos L, Malinina L, J Biomol Struct Dyn. 1997 Aug;15(1):151-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9283988 9283988]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Campos, L.]] | + | |
| - | [[Category: Fernandez, L Campos L G.]] | + | |
| - | [[Category: Pyshnyi, D.]] | + | |
| - | [[Category: Subirana, J A.]] | + | |
| - | [[Category: Verdaguer, N.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:51 2008''
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