› 6n6c

X-ray diffraction
1.62Å resolution

Vibrio cholerae Oligoribonuclease bound to pAA

Released:
DOI: 10.2210/pdb6n6c/pdb
PDB entry 6n6c coloured by chain, front view.
PDB entry 6n6c coloured by chain, side view.
PDB entry 6n6c coloured by chain, top view.
Source organisms:
Primary publication:
A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT
Elife 8 (2019)
PMID: 31225796

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192126 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Oligoribonuclease Chain: A
Molecule details ›
Chain: A
Length: 181 amino acids
Theoretical weight: 20.95 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KV17 (Residues: 1-181; Coverage: 100%)
Gene names: VC_0341, orn
Sequence domains: Exonuclease
RNA (5'-R(P*AP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 2 nucleotides
Theoretical weight: 613 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P3221
Unit cell:
a: 89.375Å b: 89.375Å c: 59.451Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.147 0.146 0.155
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Nucleotide second messengers in bacterial decision making.
Thompson et al. (2020)
3 more

1 mention without citation

A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.
Kim et al. (2019)