› 3ey1

X-ray diffraction
1.6Å resolution

A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution

Released:
DOI: 10.2210/pdb3ey1/pdb
PDB entry 3ey1 coloured by chain, front view.
PDB entry 3ey1 coloured by chain, side view.
PDB entry 3ey1 coloured by chain, top view.
Source organism: Halalkalibacterium halodurans
Primary publication:
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M
Chem Commun (Camb) 2017-9 (2009)
PMID: 19333476

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116224 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 138 amino acids
Theoretical weight: 15.92 KDa
Source organism: Alkalihalobacillus halodurans
Expression system: Not provided
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.73 KDa
Source organism: Halalkalibacterium halodurans
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 3 x GOL
1 modified residue:
Ligand USM 2 x USM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2
Unit cell:
a: 81.93Å b: 66.62Å c: 38.77Å
α: 90° β: 103.3° γ: 90°
R-values:
R R work R free
0.193 0.193 0.261
Expression system: Not provided

Quick links

Citations

3 review citations

The many twists and turns of DNA: template, telomere, tool, and target.
Egli et al. (2010)
2 more

3 mentions without citation

Mono a Mano: ZBP1's Love-Hate Relationship with the Kissing Virus.
Herbert et al. (2022)
2 more