2GPM

Crystal structure of an RNA racemate

Summary for 2GPM

• Entry DOI: 10.2210/pdb2gpm/pdb
• Related: 2G32 2GQ4 2GQ5 2GQ6 2GQ7
• Descriptor: RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3'), RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3'), CALCIUM ION, ... (4 entities in total)
• Functional Keywords: double helix, racemate, rna
• Total number of polymer chains: 4
• Total formula weight: 10470.78

Authors

Rypniewski, W.,Vallazza, M.,Perbandt, M.,Klussmann, S.,Betzel, C.,Erdmann, V.A. (deposition date: 2006-04-18, release date: 2006-06-27, Last modification date: 2024-04-03)

Primary citation

Rypniewski, W.,Vallazza, M.,Perbandt, M.,Klussmann, S.,Delucas, L.J.,Betzel, C.,Erdmann, V.A.
The first crystal structure of an RNA racemate.
Acta Crystallogr.,Sect.D, 62:659-664, 2006

PubMed Abstract: The racemate of the RNA duplex r(CUGGGCGG).r(CCGCCUGG) from Thermus flavus 5S rRNA has been crystallized and examined by X-ray crystallography. The space group is P1(_) with approximate unit-cell parameters a = 26.5, b = 38.0, c = 45.4 Angstrom, alpha = 113.1, beta = 100.5, gamma = 93.3 degrees. The structure was solved by molecular replacement. There are four RNA duplexes in the unit cell. The crystal lattice consists of columns of RNA duplexes. The duplexes are stacked end-to-end and are stabilized by intermolecular base-stacking interactions. Within each column the L-duplexes and D-duplexes are stacked alternately. Every other duplex in each stack has two alternative conformations, approximately equally occupied, corresponding to molecules oriented in opposite directions. Neighbouring columns are related by the crystallographic centre of symmetry. The unit cell also contains approximately 250 ordered water molecules and six ordered calcium ions. A glycerol molecule is visible in the minor groove interacting with a guanosine residue.

PubMed: 16699193
DOI: 10.1107/S090744490601359X

Experimental method

X-RAY DIFFRACTION (1.4 Å)