› 5gkf

X-ray diffraction
2.8Å resolution

Structure of EndoMS-dsDNA1' complex

Released:
DOI: 10.2210/pdb5gkf/pdb
PDB entry 5gkf coloured by chain, front view.
PDB entry 5gkf coloured by chain, side view.
PDB entry 5gkf coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T
Structure 24 1960-1971 (2016)
PMID: 27773688

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118702 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease NucS Chains: A, B
Molecule details ›
Chains: A, B
Length: 252 amino acids
Theoretical weight: 28.6 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JER9 (Residues: 1-252; Coverage: 100%)
Gene names: TK1898, nucS
Sequence domains:
DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.52 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MPD 5 x MPD
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P6122
Unit cell:
a: 92.44Å b: 92.44Å c: 404.32Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.171 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

DNA repair in the archaea-an emerging picture.
White et al. (2018)
8 more

1 mention without citation

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes.
Niu et al. (2020)