› 3qxs

X-ray diffraction
1.35Å resolution

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP

Released:
DOI: 10.2210/pdb3qxs/pdb
PDB entry 3qxs coloured by chain, front view.
PDB entry 3qxs coloured by chain, side view.
PDB entry 3qxs coloured by chain, top view.
Source organism: Helicobacter pylori 26695
Primary publication:
Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W
FEBS J 279 1093-105 (2012)
PMID: 22284390

Function and Biology Details

Reaction catalysed: 
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127684 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ATP-dependent dethiobiotin synthetase BioD Chain: A
Molecule details ›
Chain: A
Length: 242 amino acids
Theoretical weight: 27.15 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O24872 (Residues: 1-218; Coverage: 100%)
Gene names: HP_0029, bioD
Sequence domains: AAA domain
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand EDO 11 x EDO
Ligand ANP 1 x ANP
Ligand MG 1 x MG
Ligand NO3 1 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: C2
Unit cell:
a: 82.085Å b: 37.582Å c: 69.232Å
α: 90° β: 101.28° γ: 90°
R-values:
R R work R free
0.144 0.143 0.165
Expression system: Escherichia coli BL21

Quick links

Citations

4 citation in other articles

Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.
Porebski et al. (2018)
3 more

1 mention without citation

Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
Porebski et al. (2012)