1qc0
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1qc0 |SIZE=350|CAPTION= <scene name='initialview01'>1qc0</scene>, resolution 1.55Å | |PDB= 1qc0 |SIZE=350|CAPTION= <scene name='initialview01'>1qc0</scene>, resolution 1.55Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NH4:AMMONIUM ION'>NH4</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1qcu|1QCU]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qc0 OCA], [http://www.ebi.ac.uk/pdbsum/1qc0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qc0 RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Shah, S A.]] | [[Category: Shah, S A.]] | ||
[[Category: Steitz, T A.]] | [[Category: Steitz, T A.]] | ||
| - | [[Category: NH4]] | ||
[[Category: a-rna structure]] | [[Category: a-rna structure]] | ||
[[Category: ribonucleic acid]] | [[Category: ribonucleic acid]] | ||
| - | ''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 23:11:39 2008'' |
Revision as of 20:11, 30 March 2008
| |||||||
| , resolution 1.55Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 1QCU
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF A 19 BASE PAIR COPY CONTROL RELATED RNA DUPLEX
Overview
The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. Crystals containing the 18mers 5'-CA CCGUUGGUAGCGGUGC-3' and 5'-CACCGCUACCAACGGUGC-3' diffract to 1.20 A resolution while those containing the 19mers 5'-GCACCGUUGGUAGCGGUGC-3' and 5'-GCACCGCUACCAACGGUGC-3' diffract to 1.55 A resolution. Both duplexes are standard A form, with Watson-Crick base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 A structure dramatically improved refinement statistics, resulting in a final R(free) of 15.0% and a crystallographic R-factor of 11.6%. Perhaps surprisingly, these crystals of the 18 base pair RNA exhibit a 36-fold static disorder, resulting in a structure with a single sugar-phosphate backbone conformation and an averaged base composition at each residue. Since the sugar-phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no sequence-dependent variation in the structure. The average ribose pucker amplitude is 45.8 degrees for the 18 base pair structure and 46.4 degrees for the 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structures. A standard RNA water structure, based on analysis of the hydration of these crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824], has been derived, which has allowed us to predict water positions in lower resolution RNA crystal structures. We report a new RNA packing motif, in which three pro-S(p) phosphate oxygens interact with an ammonium ion.
About this Structure
1QC0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structures of two plasmid copy control related RNA duplexes: An 18 base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution., Klosterman PS, Shah SA, Steitz TA, Biochemistry. 1999 Nov 9;38(45):14784-92. PMID:10555960
Page seeded by OCA on Sun Mar 30 23:11:39 2008
