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| - | [[Image:318d.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURES OF D(CCGGGCC(BR)5CGG)-HEXAGONAL FORM== |
| - | |PDB= 318d |SIZE=350|CAPTION= <scene name='initialview01'>318d</scene>, resolution 2.000Å
| + | <StructureSection load='318d' size='340' side='right'caption='[[318d]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene> | + | <table><tr><td colspan='2'>[[318d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=318D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=318D 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]] 2Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</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=318d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=318d OCA], [https://pdbe.org/318d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=318d RCSB], [https://www.ebi.ac.uk/pdbsum/318d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=318d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=318d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=318d OCA], [http://www.ebi.ac.uk/pdbsum/318d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=318d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURES OF D(CCGGGCC(BR)5CGG)-HEXAGONAL FORM'''
| + | [[Category: Sundaralingam M]] |
| - | | + | [[Category: Tippin DB]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | The A-DNA decamer d(CCGGGCCm5CGG) crystallizes in the presence of spermine in three polymorphic forms and with one duplex in the asymmetric unit: hexagonal (P6(1)), unit cell of 55.0 A x 55.0 A x 45.9 A; orthorhombic (P2(1)2(1)2(1)), unit cell of 24.8 A x 44.6 A x 48.0 A, and a second orthorhombic (P2(1)2(1)2(1)), unit cell of 23.6 A x 40.8 A x 43.4 A. The reduction in cell volume among the three different forms is accompanied by a large reduction in solvent content (67% versus 40% versus 24%) and a significant reduction in volume per base-pair (2005 A(3) versus 1325 A(3) versus 1048 A(3)). There is also a concomitant increase in the number of bound spermine molecules per duplex (0 versus 1 versus 2) as well as an increase in DNA bending (10 degrees versus 16 degrees versus 31 degrees), which correspond to major groove widths of 8.0 A versus 4.5 A versus 1.3 A, respectively. The P6(1) crystal form, which represents a new space group for A-DNA decamers, supports one of the most hydrated and extended DNA duplexes to date, while the second orthorhombic form supports one of the least-hydrated and most-condensed non-Z-DNA duplexes. The unmethylated analogue d(CCGGGCCCGG), the double-methyl derivative d(Cm5CGGGCCm5CGG) and the bromine derivative d(CCGGGCC(Br)5CGG) also crystallize in at least two of the aforementioned conformations, and all nine crystal structures were determined. We report, in detail, on the three crystal structures of d(CCGGGCCm5CGG) and the effects of methylation and spermine binding on A-DNA conformation.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 318D 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=318D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Nine polymorphic crystal structures of d(CCGGGCCCGG), d(CCGGGCCm5CGG), d(Cm5CGGGCCm5CGG) and d(CCGGGCC(Br)5CGG) in three different conformations: effects of spermine binding and methylation on the bending and condensation of A-DNA., Tippin DB, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1171-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9150405 9150405]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Tippin, D B.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: double helix]]
| + | |
| - | [[Category: modified]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:17 2008''
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