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X-ray diffraction
2.2Å resolution

Crystal structure of staphylococcal nuclease variant E75Q/D21N/T33V/T41I/S59A/P117G/S128A at 100 K

Released:
DOI: 10.2210/pdb2qdb/pdb
PDB entry 2qdb coloured by chain, front view.
PDB entry 2qdb coloured by chain, side view.
PDB entry 2qdb coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease.
Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE
J Mol Biol 379 1045-62 (2008)
PMID: 18499123

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132790 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nuclease A Chain: A
Molecule details ›
Chain: A
Length: 149 amino acids
Theoretical weight: 16.78 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P00644 (Residues: 83-231; Coverage: 73%)
Gene name: nuc
Sequence domains: Staphylococcal nuclease homologue
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P41
Unit cell:
a: 48.668Å b: 48.668Å c: 63.277Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.239 0.276
Expression system: Escherichia coli

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Citations

6 review citations

Protein ionizable groups: pK values and their contribution to protein stability and solubility.
Pace et al. (2009)
5 more