› 3gve

X-ray diffraction
1.25Å resolution

Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis

Released:
DOI: 10.2210/pdb3gve/pdb
PDB entry 3gve coloured by chain, front view.
PDB entry 3gve coloured by chain, side view.
PDB entry 3gve coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Entry authors: Kim Y, Marshall N, Cobb G, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reactions catalysed: 
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
A 3'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 3'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128526 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Trifunctional nucleotide phosphoesterase protein YfkN Chains: A, B
Molecule details ›
Chains: A, B
Length: 341 amino acids
Theoretical weight: 37.48 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: O34313 (Residues: 37-374; Coverage: 24%)
Gene names: BSU07840, yfkN
Sequence domains: Calcineurin-like phosphoesterase
Structure domains: Purple Acid Phosphatase; chain A, domain 2

Ligands and Environments

3 bound ligands:
Ligand MN 2 x MN
Ligand MG 3 x MG
Ligand CIT 2 x CIT
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 67.091Å b: 92.505Å c: 50.316Å
α: 90° β: 89.94° γ: 90°
R-values:
R R work R free
0.154 0.154 0.163
Expression system: Escherichia coli

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