› 3twh

X-ray diffraction
1.79Å resolution

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant

Released:
DOI: 10.2210/pdb3twh/pdb
PDB entry 3twh coloured by chain, front view.
PDB entry 3twh coloured by chain, side view.
PDB entry 3twh coloured by chain, top view.
Source organism: Halalkalibacterium halodurans
Primary publication:
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.
Abdur R, Gerlits OO, Gan J, Jiang J, Salon J, Kovalevsky AY, Chumanevich AA, Weber IT, Huang Z
Acta Crystallogr D Biol Crystallogr 70 354-61 (2014)
PMID: 24531469

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-116947 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 138 amino acids
Theoretical weight: 15.92 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.95 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.88 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand PO4 1 x PO4
1 modified residue:
Ligand SDG 2 x SDG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: C2
Unit cell:
a: 80.66Å b: 37.819Å c: 61.937Å
α: 90° β: 96.6° γ: 90°
R-values:
R R work R free
0.177 0.175 0.208
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

2 review citations

Recent Methods for Purification and Structure Determination of Oligonucleotides.
Zhang et al. (2016)
1 more

2 mentions without citation

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