› 3va3

X-ray diffraction
2.71Å resolution

Crystal structure of RNase T in complex with a duplex DNA product (stem loop DNA with 2 nucleotide 3' overhang)

Released:
DOI: 10.2210/pdb3va3/pdb
PDB entry 3va3 coloured by chain, front view.
PDB entry 3va3 coloured by chain, side view.
PDB entry 3va3 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes.
Hsiao YY, Duh Y, Chen YP, Wang YT, Yuan HS
Nucleic Acids Res 40 8144-54 (2012)
PMID: 22718982

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117039 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease T Chains: A, B
Molecule details ›
Chains: A, B
Length: 235 amino acids
Theoretical weight: 25.65 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P30014 (Residues: 1-215; Coverage: 100%)
Gene names: JW1644, b1652, rnt
Sequence domains: Exonuclease
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 18 nucleotides
Theoretical weight: 5.47 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CO 2 x CO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P21212
Unit cell:
a: 100.266Å b: 112.684Å c: 57.793Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.265 0.263 0.29
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Bacterial ribonucleases and their roles in RNA metabolism.
Bechhofer et al. (2019)
3 more

4 mentions without citation

The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once.
Tsutakawa et al. (2014)
3 more