› 3pdw

X-ray diffraction
1.6Å resolution

Crystal structure of putative p-nitrophenyl phosphatase from Bacillus subtilis

Released:
DOI: 10.2210/pdb3pdw/pdb
PDB entry 3pdw coloured by chain, front view.
PDB entry 3pdw coloured by chain, side view.
PDB entry 3pdw coloured by chain, top view.
Source organism: Bacillus subtilis
Entry authors: Fedorov AA, Fedorov EV, Toro R, Sauder JM, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128415 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'-nucleotidase YutF Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 29.2 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O32125 (Residues: 2-256; Coverage: 100%)
Gene names: BSU32290, yutF
Sequence domains: haloacid dehalogenase-like hydrolase
Structure domains: HAD superfamily/HAD-like

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: C2
Unit cell:
a: 94.19Å b: 38.878Å c: 81.031Å
α: 90° β: 93.04° γ: 90°
R-values:
R R work R free
0.186 0.184 0.211
Expression system: Escherichia coli

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