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| [[Image:1bna.jpg|left|200px]]<br /><applet load="1bna" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="1bna, resolution 1.900Å" />
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| '''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS'''<br />
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| ==Overview== | | ==STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS== |
| The crystal structure of the synthetic DNA dodecamer, d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R =, 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly, more than one complete turn of right-handed double-stranded B helix. The, two ends of the helix overlap and interlock minor grooves with neighboring, molecules up and down a 2(1) screw axis, producing a 19 degrees bend in, helix axis over the 11-base-pair steps of the dodecamer. In the center of, the molecule, where perturbation is least, the helix has a mean rotation, of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller, twist (total dihedral angle between base planes) between A . T base pairs, in the center of the molecule is 17.3 degrees, and that between C . G, pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring, conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo, position with delta avg = 123 degrees and a range of 79 degrees to 157, degrees. Purine sugars cluster at high delta values, and pyrimidine sugars, cluster at lower delta. A tendency toward 2-fold symmetry in sugar, conformation about the center of the molecule is detectable in spite of, the destruction of ideal 2-fold symmetry by the molecular bending. More, strikingly, sugar conformations of paired based appear to follow a, "principle of anticorrelation," with delta values lying approximately the, same distance to either side of the center value, delta = 123 degrees., This same anticorrelation is also observed in other DNA and DNA . RNA, structures.
| | <StructureSection load='1bna' size='340' side='right'caption='[[1bna]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1bna]] is a 2 chain structure. The November 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_11 10.2210/rcsb_pdb/mom_2001_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BNA FirstGlance]. <br> |
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bna OCA], [https://pdbe.org/1bna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bna RCSB], [https://www.ebi.ac.uk/pdbsum/1bna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bna ProSAT]</span></td></tr> |
| | </table> |
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| ==About this Structure== | | ==See Also== |
| 1BNA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. The following page contains interesting information on the relation of 1BNA with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA].
| | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| Structure of a B-DNA dodecamer: conformation and dynamics., Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE, Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=6941276 6941276]
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| [[Category: DNA]] | | [[Category: DNA]] |
| [[Category: Protein complex]] | | [[Category: Large Structures]] |
| [[Category: Broka, C.]] | | [[Category: RCSB PDB Molecule of the Month]] |
| [[Category: Dickerson, R.E.]] | | [[Category: Broka C]] |
| [[Category: Drew, H.R.]] | | [[Category: Dickerson RE]] |
| [[Category: Itakura, K.]] | | [[Category: Drew HR]] |
| [[Category: Takano, T.]] | | [[Category: Itakura K]] |
| [[Category: Tanaka, S.]] | | [[Category: Takano T]] |
| [[Category: Wing, R.M.]] | | [[Category: Tanaka S]] |
| [[Category: b-dna]]
| | [[Category: Wing RM]] |
| [[Category: double helix]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:32:43 2008''
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