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| - | [[Image:440d.gif|left|200px]] | |
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| - | {{Structure
| + | ==HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-DNA MODEL OF POLY(DG).POLY(DC)== |
| - | |PDB= 440d |SIZE=350|CAPTION= <scene name='initialview01'>440d</scene>, resolution 1.10Å
| + | <StructureSection load='440d' size='340' side='right'caption='[[440d]], [[Resolution|resolution]] 1.10Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <table><tr><td colspan='2'>[[440d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=440D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=440D 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]] 1.1Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=440d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=440d OCA], [https://pdbe.org/440d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=440d RCSB], [https://www.ebi.ac.uk/pdbsum/440d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=440d ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=440d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=440d OCA], [http://www.ebi.ac.uk/pdbsum/440d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=440d RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Gao Y-G]] |
| - | '''HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-DNA MODEL OF POLY(DG).POLY(DC)'''
| + | [[Category: Robinson HH]] |
| - | | + | [[Category: Wang AH-J]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | A-DNA conformation is favored by guanine-rich sequences, such as (dG)n x (dC)n, or under low-humidity conditions. Earlier A-DNA crystal structures revealed some conformational variations which may be the result of sequence-dependent effects and/or crystal packing forces. Here we report the high-resolution crystal structure of d(AGGGGCCCCT) in two crystal forms (either in the P212121 or the P6122 space group) to gain insights into the conformation and dynamics of the (dG)n x (dC)n sequence. The P212121 form has been analyzed using data to 1.1 A resolution by the anisotropic temperature factor refinement procedure of the SHELX97 program. Such analysis affords us with the detailed geometric, conformational and motional property of an A-DNA structure. The backbone torsional angles fall in a narrow range, except for the alpha/gamma angles which have two distinct combinations (gauche-/gauche+ or trans/trans). An A-DNA model of poly(dG) x poly(dC) has been constructed using the conformational parameters derived from the crystal structure of the P212121 form. In the crystal structure of the P6122 space group, the central eight base pairs of the decamer adopt A-DNA conformation with the two terminal nucleotides flipped out to form base pairs with the neighboring nucleotides. Comparison of the A-DNA structure of the same sequence from two different crystal forms, reinforced the conclusion that molecules crystallized in the same space group have a more similar conformation, whereas the same molecule crystallized in different space groups has different (local) conformations.
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| - | ==About this Structure==
| + | |
| - | 440D 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=440D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC)., Gao YG, Robinson H, Wang AH, Eur J Biochem. 1999 Apr;261(2):413-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10215851 10215851]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Gao, Y G.]] | + | |
| - | [[Category: Robinson, H H.]] | + | |
| - | [[Category: Wang, A H.J.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: duplex]]
| + | |
| - | [[Category: high resolution]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:14 2008''
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