› 5on4

X-ray diffraction
2.3Å resolution

Crystal structure of NikA in complex with Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)

Released:
DOI: 10.2210/pdb5on4/pdb
PDB entry 5on4 coloured by chain, front view.
PDB entry 5on4 coloured by chain, side view.
PDB entry 5on4 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions.
Lopez S, Rondot L, Leprêtre C, Marchi-Delapierre C, Ménage S, Cavazza C
J Am Chem Soc 139 17994-18002 (2017)
PMID: 29148757

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
Molecule details ›
Chains: A, B
Length: 502 amino acids
Theoretical weight: 56.36 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
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

3 bound ligands:
Ligand FE 2 x FE
Ligand 9YK 2 x 9YK
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 86.69Å b: 94.121Å c: 129.545Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.221 0.267
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere.
Van Stappen et al. (2022)
2 more