› 1fiu

X-ray diffraction
1.6Å resolution

TETRAMERIC RESTRICTION ENDONUCLEASE NGOMIV IN COMPLEX WITH CLEAVED DNA

Released:
DOI: 10.2210/pdb1fiu/pdb
PDB entry 1fiu coloured by chain, front view.
PDB entry 1fiu coloured by chain, side view.
PDB entry 1fiu coloured by chain, top view.
Source organism: Neisseria gonorrhoeae
Primary publication:
Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA.
Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R
Nat Struct Biol 7 792-9 (2000)
PMID: 10966652

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113803 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction enzyme NgoMIV Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 286 amino acids
Theoretical weight: 31.81 KDa
Source organism: Neisseria gonorrhoeae
Expression system: Escherichia coli
UniProt:
  • Canonical: P31032 (Residues: 1-286; Coverage: 100%)
Gene name: ngoMIVR
Sequence domains: NgoMIV restriction enzyme
Structure domains: Type-2 restriction enzyme NgoMIV
DNA (5'-D(*TP*GP*CP*G)-3') Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 4 nucleotides
Theoretical weight: 1.21 KDa
Source organism: Neisseria gonorrhoeae
Expression system: Not provided
DNA (5'-D(P*CP*CP*GP*GP*CP*GP*C)-3') Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: Neisseria gonorrhoeae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 8 x MG
Ligand ACY 4 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P212121
Unit cell:
a: 90.4Å b: 91.13Å c: 149.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.173 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Type II restriction endonucleases--a historical perspective and more.
Pingoud et al. (2014)
4 more

20 mentions without citation

Structure and function of type II restriction endonucleases.
Pingoud et al. (2001)
19 more