› 3o0f

X-ray diffraction
1.94Å resolution

Crystal structure of a putative metal-dependent phosphoesterase (BAD_1165) from bifidobacterium adolescentis atcc 15703 at 1.94 A resolution

Released:
DOI: 10.2210/pdb3o0f/pdb
PDB entry 3o0f coloured by chain, front view.
PDB entry 3o0f coloured by chain, side view.
PDB entry 3o0f coloured by chain, top view.
Source organism: Bifidobacterium adolescentis ATCC 15703
Primary publication:
Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.
Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ
Proteins 79 2146-60 (2011)
PMID: 21538547

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106537 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Polymerase/histidinol phosphatase N-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 301 amino acids
Theoretical weight: 32.86 KDa
Source organism: Bifidobacterium adolescentis ATCC 15703
Expression system: Escherichia coli
UniProt:
  • Canonical: A1A2L3 (Residues: 1-300; Coverage: 100%)
Gene name: BAD_1165
Sequence domains: PHP domain
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand AMP 1 x AMP
Ligand ZN 1 x ZN
Ligand FE 2 x FE
Ligand PO4 1 x PO4
Ligand EDO 2 x EDO
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P65
Unit cell:
a: 103.341Å b: 103.341Å c: 54.744Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.161 0.16 0.192
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Biochemical functional predictions for protein structures of unknown or uncertain function.
Mills et al. (2015)
7 other articles

4 mentions without citation

Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.
Han et al. (2011)
3 more