› 2hzv

X-ray diffraction
3.1Å resolution

NikR-operator DNA complex

Released:
DOI: 10.2210/pdb2hzv/pdb
PDB entry 2hzv coloured by chain, front view.
PDB entry 2hzv coloured by chain, side view.
PDB entry 2hzv coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
NikR-operator complex structure and the mechanism of repressor activation by metal ions.
Schreiter ER, Wang SC, Zamble DB, Drennan CL
Proc Natl Acad Sci U S A 103 13676-81 (2006)
PMID: 16945905

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115375 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Nickel-responsive regulator Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 133 amino acids
Theoretical weight: 15.21 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6Z6 (Residues: 1-133; Coverage: 100%)
Gene names: JW3446, b3481, nikR, yhhG
Sequence domains:
Structure domains:
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3' Chains: I, K
Molecule details ›
Chains: I, K
Length: 30 nucleotides
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3' Chains: J, L
Molecule details ›
Chains: J, L
Length: 30 nucleotides
Theoretical weight: 9.23 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NI 8 x NI
Ligand K 11 x K
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 197.203Å b: 76.132Å c: 132.092Å
α: 90° β: 110.27° γ: 90°
R-values:
R R work R free
0.261 0.261 0.303
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage.
Thauer et al. (2010)
11 more

17 mentions without citation

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