› 2y3y

X-ray diffraction
2.39Å resolution

Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH

Released:
DOI: 10.2210/pdb2y3y/pdb
PDB entry 2y3y coloured by chain, front view.
PDB entry 2y3y coloured by chain, side view.
PDB entry 2y3y coloured by chain, top view.
Source organisms:
Primary publication:
Holo-Ni2+ Helicobacter pylori NikR contains four square-planar nickel-binding sites at physiological pH.
Benini S, Cianci M, Ciurli S
Dalton Trans 40 7831-3 (2011)
PMID: 21725560

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo tetramer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-110295 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Putative nickel-responsive regulator Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 91 amino acids
Theoretical weight: 10.43 KDa
Source organism: Helicobacter pylori G27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B5Z8Y5 (Residues: 58-148; Coverage: 62%)
Gene name: HPG27_1286
Sequence domains: NikR C terminal nickel binding domain
Structure domains: ACT-like. Chain A, domain 2
UNDECAPEPTIDE-GSSSGSASGAG Chain: Q
Molecule details ›
Chain: Q
Length: 11 amino acids
Theoretical weight: 824 Da
Source organism: unidentified

Ligands and Environments

3 bound ligands:
Ligand NI 4 x NI
Ligand EPE 2 x EPE
Ligand PEG 3 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X12
Spacegroup: P43
Unit cell:
a: 72.97Å b: 72.97Å c: 116.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.229 0.279
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Metal site occupancy and allosteric switching in bacterial metal sensor proteins.
Guerra et al. (2012)
5 more

1 mention without citation

Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.
West et al. (2012)