› 6ymg

X-ray diffraction
3.14Å resolution

VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA

Released:
DOI: 10.2210/pdb6ymg/pdb
Model geometry
Fit model/data
PDB entry 6ymg coloured by chain, front view.
PDB entry 6ymg coloured by chain, side view.
PDB entry 6ymg coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.
Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M
OpenAccess logo Nucleic Acids Res 49 1708-1723 (2021)
PMID: 33450012

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-236851 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HNH endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 35.39 KDa
Source organism: Vibrio campbellii
Expression system: Escherichia coli BL21(DE3)
DNA (5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*A)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: synthetic construct
Expression system: synthetic construct
DNA (5'-D(P*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3') Chains: D, F

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand SO4 9 x SO4
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6122
Unit cell:
a: 81.111Å b: 81.111Å c: 617.307Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.243 0.242 0.266
Expression systems:
  • Escherichia coli BL21(DE3)
  • synthetic construct

Quick links

Citations

2 citation in other articles

A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease.
Birkholz et al. (2022)
1 more

1 mention without citation

Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.
Pastor et al. (2021)