› 5swm

X-ray diffraction
1.5Å resolution

BACILLUS HALODURANS RNASE H MUTANT D132N IN COMPLEX WITH 12-MER FRNA/DNA HYBRID

Released:
DOI: 10.2210/pdb5swm/pdb
Model geometry
Fit model/data
PDB entry 5swm coloured by chain, front view.
PDB entry 5swm coloured by chain, side view.
PDB entry 5swm coloured by chain, top view.
Source organisms:
Primary publication:
Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid.
Pallan PS, Prakash TP, de Leon AR, Egli M
Biochemistry 55 5321-5 (2016)
PMID: 27611889

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119122 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chains: A, B
Molecule details ›
Chains: A, B
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Alkalihalobacillus halodurans
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (12-MER) Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.77 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (12-MER) Chain: C

Ligands and Environments

4 bound ligands:
Ligand NA 1 x NA
Ligand CL 1 x CL
Ligand PEG 1 x PEG
Ligand GOL 1 x GOL
5 modified residues:
Ligand GF2 2 x GF2
Ligand AF2 3 x AF2
Ligand CFZ 4 x CFZ
Ligand UFT 3 x UFT
Ligand BRU 1 x BRU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P1
Unit cell:
a: 37.474Å b: 44.5Å c: 62.174Å
α: 84.42° β: 89.9° γ: 65.1°
R-values:
R R work R free
0.162 0.161 0.185
Expression systems:
  • Alkalihalobacillus halodurans
  • Not provided

Quick links

Citations

4 review citations

Synthesis and biological applications of fluoro-modified nucleic acids.
Guo et al. (2017)
3 more

1 mention without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)