309d: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[309d]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=273d 273d]. The November 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Designed DNA Crystal'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_11 10.2210/rcsb_pdb/mom_2009_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=309D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=309D FirstGlance]. <br> | <table><tr><td colspan='2'>[[309d]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=273d 273d]. The November 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Designed DNA Crystal'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_11 10.2210/rcsb_pdb/mom_2009_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=309D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=309D FirstGlance]. <br> | ||
</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=309d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=309d OCA], [https://pdbe.org/309d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=309d RCSB], [https://www.ebi.ac.uk/pdbsum/309d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=309d ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</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=309d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=309d OCA], [https://pdbe.org/309d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=309d RCSB], [https://www.ebi.ac.uk/pdbsum/309d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=309d ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: Dewan | [[Category: Dewan JC]] | ||
[[Category: Qiu | [[Category: Qiu HX]] | ||
[[Category: Seeman | [[Category: Seeman NC]] | ||
Revision as of 13:28, 27 September 2023
A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGTA DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT
Structural highlights
Publication Abstract from PubMedThe crystal structure of d-CGACGATCGT has been determined to a resolution of 2.6 A. The molecule was synthesized by standard phosphoramidite procedures, and purified by anion-exchange HPLC. Crystals are monolclinic, space group P2(1), with unit cell dimensions, a = 26.45 A, b = 34.66 A, c = 32.17 A, beta = 113.45 degrees and Z = 4, containing a B-DNA double helix in each crystallographic asymmetric unit. The structure was solved using molecular replacement, aided by an isomorphous derivative, in which a bromine atom was attached to the 5 position of cytosine 8. Problems of fit between the search model and the structure ultimately obtained necessitated the use of Patterson correlation procedures between the determination of the orientation and the translation of the molecule. In all, 69 solvent molecules have been identified, and the structure has been refined to an R-factor of 0.214, using the 1421 reflections with F > 2sigma(F), collected at -120 degrees C. The sequence produces a molecule containing eight Watson-Crick base-pairs and a two-nucleotide 5'-sticky end at each end of the duplex. The sticky ends cohere with one another, so the molecules form continuous 10-fold double helices throughout the crystal, with each strand being interrupted by inherent staggered nicks. The relative angular relationships between helices in the structure differ from each other; most of the arrangements differ from Holliday junctions, whose rotational orientations are phased by a crossover and which are modeled to contain double helices that are exactly parallel or antiparallel. However, one helical juxtaposition in this crystal is similar to the alignment of double helices in parallel Holliday junctions. A survey of DNA decamers that also form infinite helices in crystals reveals relationships that approximate both parallel and antiparallel Holliday junction alignments. A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT.,Qiu H, Dewan JC, Seeman NC J Mol Biol. 1997 Apr 11;267(4):881-98. PMID:9135119[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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