› 5yi3

X-ray diffraction
2.9Å resolution

Structure of Lactococcus lactis ZitR, C30S mutant in complex with DNA

Released:
DOI: 10.2210/pdb5yi3/pdb
PDB entry 5yi3 coloured by chain, front view.
PDB entry 5yi3 coloured by chain, side view.
PDB entry 5yi3 coloured by chain, top view.
Source organisms:
Primary publication:
Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.
Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen PR
Proc Natl Acad Sci U S A 114 13661-13666 (2017)
PMID: 29229866

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119438 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
HTH marR-type domain-containing protein Chains: A, B, E, F, I, J, M, N
Molecule details ›
Chains: A, B, E, F, I, J, M, N
Length: 146 amino acids
Theoretical weight: 16.43 KDa
Source organism: Lactococcus lactis subsp. lactis Il1403
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9CDU5 (Residues: 1-145; Coverage: 100%)
Gene names: L168265, zitR
Sequence domains: MarR family
DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3') Chains: C, D, G, H, K, L, O, P
Molecule details ›
Chains: C, D, G, H, K, L, O, P
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Lactococcus lactis
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 89.522Å b: 103.058Å c: 104.855Å
α: 90° β: 94.2° γ: 90°
R-values:
R R work R free
0.208 0.205 0.262
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Bacterial zinc uptake regulator proteins and their regulons.
Mikhaylina et al. (2018)
4 more

3 mentions without citation

Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.
Zhu et al. (2017)
2 more