› 1rxq

X-ray diffraction
1.7Å resolution

YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

Released:
DOI: 10.2210/pdb1rxq/pdb
PDB entry 1rxq coloured by chain, front view.
PDB entry 1rxq coloured by chain, side view.
PDB entry 1rxq coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology.
Rajan SS, Yang X, Shuvalova L, Collart F, Anderson WF
Biochemistry 43 15472-9 (2004)
PMID: 15581359

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128308 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative metal-dependent hydrolase YfiT Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 178 amino acids
Theoretical weight: 20.89 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O31562 (Residues: 1-178; Coverage: 100%)
Gene names: BSU08390, yfiT
Sequence domains: DinB superfamily
Structure domains: dinb family like domain

Ligands and Environments

6 bound ligands:
Ligand NI 4 x NI
Ligand GLU 1 x GLU
Ligand SER 2 x SER
Ligand ALA 1 x ALA
Ligand THR 1 x THR
Ligand GLY 1 x GLY
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P1
Unit cell:
a: 46.37Å b: 50.42Å c: 89.41Å
α: 104.38° β: 90.61° γ: 112.05°
R-values:
R R work R free
0.188 0.186 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 citation in other articles

Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex.
Vorontsov et al. (2011)
7 more

5 mentions without citation

The DinB superfamily includes novel mycothiol, bacillithiol, and glutathione S-transferases.
Newton et al. (2011)
4 more