1d13
From Proteopedia
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|PDB= 1d13 |SIZE=350|CAPTION= <scene name='initialview01'>1d13</scene>, resolution 2.000Å | |PDB= 1d13 |SIZE=350|CAPTION= <scene name='initialview01'>1d13</scene>, resolution 2.000Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d13 OCA], [http://www.ebi.ac.uk/pdbsum/1d13 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d13 RCSB]</span> | ||
}} | }} | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:32:24 2008'' |
Revision as of 16:32, 30 March 2008
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| , resolution 2.000Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
MOLECULAR STRUCTURE OF AN A-DNA DECAMER D(ACCGGCCGGT)
Overview
The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.
About this Structure
1D13 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Molecular structure of an A-DNA decamer d(ACCGGCCGGT)., Frederick CA, Quigley GJ, Teng MK, Coll M, Van der Marel GA, Van Boom JH, Rich A, Wang AH, Eur J Biochem. 1989 May 1;181(2):295-307. PMID:2714286
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