117d: Difference between revisions
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==CRYSTAL AND MOLECULAR STRUCTURE OF THE ALTERNATING DODECAMER D(GCGTACGTACGC) IN THE A-DNA FORM: COMPARISON WITH THE ISOMORPHOUS NON-ALTERNATING DODECAMER D(CCGTACGTACGG)== | |||
<StructureSection load='117d' size='340' side='right'caption='[[117d]], [[Resolution|resolution]] 2.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[117d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=117D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=117D 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=117d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=117d OCA], [https://pdbe.org/117d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=117d RCSB], [https://www.ebi.ac.uk/pdbsum/117d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=117d ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
== | |||
The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55A using oscillation film data. The crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one strand in the asymmetric unit, and are isomorphous with a previously described non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ gave a final R factor of 14.2% for 1089 observations. The molecule adopts the A-DNA form. The interchange of the terminal base pairs in the two dodecamers results in differences in the intermolecular contacts and may account for the differences in the bending. This dodecamer shows an axial deflection of 30 degrees, in the direction of the major groove compared to 20 degrees in 5'-CC and may be a consequence of additional contacts generated in 5'-GC by the interchange of end base pairs. The high helical axis deflection appreciably influences the local helical parameters. The molecule exhibits relatively high inclination angles, and has a narrow major groove. The helical parameters when described relative to the dyad-related hexamer halves of the molecule give more reasonable values. The crystal packing, local helical parameters, torsion angles, and hydration are described and also compared with the non-alternating 5'-CC dodecamer. | The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55A using oscillation film data. The crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one strand in the asymmetric unit, and are isomorphous with a previously described non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ gave a final R factor of 14.2% for 1089 observations. The molecule adopts the A-DNA form. The interchange of the terminal base pairs in the two dodecamers results in differences in the intermolecular contacts and may account for the differences in the bending. This dodecamer shows an axial deflection of 30 degrees, in the direction of the major groove compared to 20 degrees in 5'-CC and may be a consequence of additional contacts generated in 5'-GC by the interchange of end base pairs. The high helical axis deflection appreciably influences the local helical parameters. The molecule exhibits relatively high inclination angles, and has a narrow major groove. The helical parameters when described relative to the dyad-related hexamer halves of the molecule give more reasonable values. The crystal packing, local helical parameters, torsion angles, and hydration are described and also compared with the non-alternating 5'-CC dodecamer. | ||
Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG).,Bingman C, Jain S, Zon G, Sundaralingam M Nucleic Acids Res. 1992 Dec 25;20(24):6637-47. PMID:1480485<ref>PMID:1480485</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: Bingman | <div class="pdbe-citations 117d" style="background-color:#fffaf0;"></div> | ||
[[Category: Jain | == References == | ||
[[Category: Sundaralingam | <references/> | ||
[[Category: Zon | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Bingman C]] | |||
[[Category: Jain S]] | |||
[[Category: Sundaralingam M]] | |||
[[Category: Zon G]] | |||
Latest revision as of 13:41, 24 November 2022
CRYSTAL AND MOLECULAR STRUCTURE OF THE ALTERNATING DODECAMER D(GCGTACGTACGC) IN THE A-DNA FORM: COMPARISON WITH THE ISOMORPHOUS NON-ALTERNATING DODECAMER D(CCGTACGTACGG)CRYSTAL AND MOLECULAR STRUCTURE OF THE ALTERNATING DODECAMER D(GCGTACGTACGC) IN THE A-DNA FORM: COMPARISON WITH THE ISOMORPHOUS NON-ALTERNATING DODECAMER D(CCGTACGTACGG)
Structural highlights
Publication Abstract from PubMedThe crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55A using oscillation film data. The crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one strand in the asymmetric unit, and are isomorphous with a previously described non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ gave a final R factor of 14.2% for 1089 observations. The molecule adopts the A-DNA form. The interchange of the terminal base pairs in the two dodecamers results in differences in the intermolecular contacts and may account for the differences in the bending. This dodecamer shows an axial deflection of 30 degrees, in the direction of the major groove compared to 20 degrees in 5'-CC and may be a consequence of additional contacts generated in 5'-GC by the interchange of end base pairs. The high helical axis deflection appreciably influences the local helical parameters. The molecule exhibits relatively high inclination angles, and has a narrow major groove. The helical parameters when described relative to the dyad-related hexamer halves of the molecule give more reasonable values. The crystal packing, local helical parameters, torsion angles, and hydration are described and also compared with the non-alternating 5'-CC dodecamer. Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG).,Bingman C, Jain S, Zon G, Sundaralingam M Nucleic Acids Res. 1992 Dec 25;20(24):6637-47. PMID:1480485[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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