› 3goc

X-ray diffraction
1.6Å resolution

Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196

Released:
DOI: 10.2210/pdb3goc/pdb
PDB entry 3goc coloured by chain, front view.
PDB entry 3goc coloured by chain, side view.
PDB entry 3goc coloured by chain, top view.
Source organism: Streptomyces avermitilis MA-4680 = NBRC 14893
Entry authors: Forouhar F, Abashidze M, Hussain M, Seetharaman J, Fang F, Xiao R, Cunningham K, Ma L, Owens L, Chen CX, Everett JK, Nair R, Acton TB, Rost B, Montelione GT, Tong L, Hunt JF, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182672 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease V Chains: A, B
Molecule details ›
Chains: A, B
Length: 237 amino acids
Theoretical weight: 25.13 KDa
Source organism: Streptomyces avermitilis MA-4680 = NBRC 14893
Expression system: Escherichia coli
UniProt:
  • Canonical: Q82MH6 (Residues: 1-229; Coverage: 100%)
Gene names: SAV_1684, nfi
Sequence domains: Endonuclease V
Structure domains: archaeoglobus fulgidus dsm 4304 superfamily

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand CL 1 x CL
Ligand YES 1 x YES
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: C2
Unit cell:
a: 123.742Å b: 40.563Å c: 107.422Å
α: 90° β: 121.61° γ: 90°
R-values:
R R work R free
0.179 0.177 0.194
Expression system: Escherichia coli

Quick links