› 6owl

X-ray diffraction
2Å resolution

RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP

Released:
DOI: 10.2210/pdb6owl/pdb
PDB entry 6owl coloured by chain, front view.
PDB entry 6owl coloured by chain, side view.
PDB entry 6owl coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.
Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW
J Am Chem Soc 142 2317-2326 (2020)
PMID: 31913615

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197116 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*R)-3') Chain: A
Molecule details ›
Chain: A
Length: 14 nucleotides
Theoretical weight: 4.51 KDa
Source organism: synthetic construct
Expression system: synthetic construct
RNA (5'-R(P*G)-3') Chains: B, C
Molecule details ›
Chains: B, C
Length: 2 nucleotides
Theoretical weight: 645 Da
Source organism: synthetic construct
Expression system: synthetic construct

Ligands and Environments

No bound ligands
2 modified residues:
Ligand LCG 1 x LCG
Ligand GAO 1 x GAO

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: R32
Unit cell:
a: 43.483Å b: 43.483Å c: 127.538Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.242 0.237 0.317
Expression system: synthetic construct

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Citations

3 review citations

Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments.
Chatragadda et al. (2021)
2 more

1 mention without citation

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.
Kim et al. (2020)