› 4j9t

X-ray diffraction
1.4Å resolution

Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61

Released:
DOI: 10.2210/pdb4j9t/pdb
PDB entry 4j9t coloured by chain, front view.
PDB entry 4j9t coloured by chain, side view.
PDB entry 4j9t coloured by chain, top view.
Source organism: Micromonospora viridifaciens
Primary publication:
Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.
Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D
J Am Chem Soc 135 13393-9 (2013)
PMID: 23924187

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
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-169775 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sialidase Chain: A
Molecule details ›
Chain: A
Length: 363 amino acids
Theoretical weight: 38.55 KDa
Source organism: Micromonospora viridifaciens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02834 (Residues: 47-407; Coverage: 59%)
Gene name: nedA
Sequence domains: BNR repeat-like domain
Structure domains: Neuraminidase

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand ARS 1 x ARS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P212121
Unit cell:
a: 46.163Å b: 79.677Å c: 83.777Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.139 0.135 0.166
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

28 review citations

Expanding and reprogramming the genetic code.
Chin JW. (2017)
27 more

2 mentions without citation

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.
Mills et al. (2013)
1 more