› 4kaz

X-ray diffraction
1.9Å resolution

Crystal structure of RNase T in complex with a Y structured DNA

Released:
DOI: 10.2210/pdb4kaz/pdb
PDB entry 4kaz coloured by chain, front view.
PDB entry 4kaz coloured by chain, side view.
PDB entry 4kaz coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS
PLoS Biol 12 e1001803 (2014)
PMID: 24594808

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117731 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease T Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 25.72 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(*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.05 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 60.675Å b: 90.58Å c: 46.621Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.218
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

2 mentions without citation

Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
Hsiao et al. (2014)
1 more