5DA6
Atomic resolution crystal structure of double-stranded RNA 32 base pairs long determined from random starting phases angles in the presence of pseudo translational symmetry using the direct methods program SIR2014.
Summary for 5DA6
| Entry DOI | 10.2210/pdb5da6/pdb |
| Related | 5D99 |
| Descriptor | RNA (32-MER), POTASSIUM ION (3 entities in total) |
| Functional Keywords | rna editing substrate, double-stranded rna, direct methods structure determination, pseudo translational symmetry, rna |
| Biological source | Trypanosoma brucei |
| Total number of polymer chains | 1 |
| Total formula weight | 10256.08 |
| Authors | Mooers, B.H.M. (deposition date: 2015-08-19, release date: 2016-04-13, Last modification date: 2024-03-06) |
| Primary citation | Mooers, B.H. Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry. Acta Crystallogr D Struct Biol, 72:477-487, 2016 Cited by PubMed Abstract: Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the l Miller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. More sensitive methods are needed for the automated detection of partial TPS. PubMed: 27050127DOI: 10.1107/S2059798316001224 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.05 Å) |
Structure validation
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