› 2bj7

X-ray diffraction
2.1Å resolution

NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES

Released:
DOI: 10.2210/pdb2bj7/pdb
PDB entry 2bj7 coloured by chain, front view.
PDB entry 2bj7 coloured by chain, side view.
PDB entry 2bj7 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition.
Chivers PT, Tahirov TH
J Mol Biol 348 597-607 (2005)
PMID: 15826657

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129705 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative nickel-responsive regulator Chains: A, B
Molecule details ›
Chains: A, B
Length: 138 amino acids
Theoretical weight: 15.83 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O58316 (Residues: 1-138; Coverage: 100%)
Gene name: PH0601
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand NI 4 x NI
Ligand EDO 2 x EDO
Ligand PG4 2 x PG4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P3221
Unit cell:
a: 109.952Å b: 109.952Å c: 79.003Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.196 0.215
Expression system: Escherichia coli BL21(DE3)

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Citations

9 review citations

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

5 mentions without citation

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea.
Darnell et al. (2020)
4 more