› 4rdm

X-ray diffraction
2.7Å resolution

Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA

Released:
DOI: 10.2210/pdb4rdm/pdb
PDB entry 4rdm coloured by chain, front view.
PDB entry 4rdm coloured by chain, side view.
PDB entry 4rdm coloured by chain, top view.
Source organism: Neisseria gonorrhoeae FA 1090
Primary publication:
Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.
Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V
OpenAccess logo Nucleic Acids Res 42 14022-30 (2014)
PMID: 25429979

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118091 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease NgoFVII Chains: A, B
Molecule details ›
Chains: A, B
Length: 178 amino acids
Theoretical weight: 20.67 KDa
Source organism: Neisseria gonorrhoeae FA 1090
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5F9M9 (Residues: 179-345; Coverage: 48%)
Gene name: NGO_0364
Sequence domains: NgoFVII C-terminal B3-like DNA-binding domain
DNA (5'-D(*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3)' Chains: C, E
Molecule details ›
Chains: C, E
Length: 15 nucleotides
Theoretical weight: 4.54 KDa
Source organism: Neisseria gonorrhoeae FA 1090
Expression system: Not provided
DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*G)-3)' Chains: D, F
Molecule details ›
Chains: D, F
Length: 15 nucleotides
Theoretical weight: 4.63 KDa
Source organism: Neisseria gonorrhoeae FA 1090
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 63.307Å b: 95.464Å c: 97.817Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.218 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 citation in other articles

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
Sasnauskas et al. (2018)
5 more

1 mention without citation

Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.
Tamulaitiene et al. (2014)