› 4i8c

X-ray diffraction
2.5Å resolution

X-ray structure of NikA in complex with Ni-(L-His)2

Released:
DOI: 10.2210/pdb4i8c/pdb
PDB entry 4i8c coloured by chain, front view.
PDB entry 4i8c coloured by chain, side view.
PDB entry 4i8c coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The binding mode of Ni-(L-His)2 in NikA revealed by X-ray crystallography.
Lebrette H, Iannello M, Fontecilla-Camps JC, Cavazza C
J Inorg Biochem 121 16-8 (2013)
PMID: 23314594

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152624 (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

6 bound ligands:
Ligand HIS 6 x HIS
Ligand NI 3 x NI
Ligand ACT 16 x ACT
Ligand GOL 8 x GOL
Ligand CL 1 x CL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P62
Unit cell:
a: 158.63Å b: 158.63Å c: 135.82Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.188 0.234
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Common themes and unique proteins for the uptake and trafficking of nickel, a metal essential for the virulence of Helicobacter pylori.
de Reuse et al. (2013)
2 more

1 mention without citation

A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens.
El Sahili et al. (2015)