› 3jyf

X-ray diffraction
2.43Å resolution

The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase bifunctional periplasmic precursor protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Released:
DOI: 10.2210/pdb3jyf/pdb
PDB entry 3jyf coloured by chain, front view.
PDB entry 3jyf coloured by chain, side view.
PDB entry 3jyf coloured by chain, top view.
Source organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Entry authors: Fan Y, Volkart L, Cobb G, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reactions catalysed: 
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

Assemblies composition:
monomeric
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108108 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase bifunctional periplasmic protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 339 amino acids
Theoretical weight: 37.36 KDa
Source organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression system: Escherichia coli
UniProt:
  • Canonical: A6THC4 (Residues: 16-354; Coverage: 53%)
Gene names: KPN_04607, cpdB
Sequence domains: Calcineurin-like phosphoesterase
Structure domains: Purple Acid Phosphatase; chain A, domain 2

Ligands and Environments

5 bound ligands:
Ligand MN 4 x MN
Ligand EPE 2 x EPE
Ligand GOL 9 x GOL
Ligand SO4 3 x SO4
Ligand TAM 1 x TAM
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P41212
Unit cell:
a: 106.041Å b: 106.041Å c: 182.967Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.179 0.231
Expression system: Escherichia coli

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