› 3e3k

X-ray diffraction
2.8Å resolution

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)

Released:
DOI: 10.2210/pdb3e3k/pdb
PDB entry 3e3k coloured by chain, front view.
PDB entry 3e3k coloured by chain, side view.
PDB entry 3e3k coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA.
Cherrier MV, Cavazza C, Bochot C, Lemaire D, Fontecilla-Camps JC
Biochemistry 47 9937-43 (2008)
PMID: 18759453

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-543040 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nickel-binding periplasmic protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 502 amino acids
Theoretical weight: 56.36 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P33590 (Residues: 23-524; Coverage: 100%)
Gene names: JW3441, b3476, nikA
Sequence domains: Bacterial extracellular solute-binding proteins, family 5 Middle
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand GOL 3 x GOL
Ligand ACT 6 x ACT
Ligand SO4 1 x SO4
Ligand HCT 3 x HCT
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P62
Unit cell:
a: 158.7Å b: 158.7Å c: 134.6Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.249 0.245 0.321
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Coordination chemistry of bacterial metal transport and sensing.
Ma et al. (2009)
8 more

1 mention without citation

Druggability analysis and structural classification of bromodomain acetyl-lysine binding sites.
Vidler et al. (2012)