› 4u0y

X-ray diffraction
1.91Å resolution

Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

Released:
DOI: 10.2210/pdb4u0y/pdb
PDB entry 4u0y coloured by chain, front view.
PDB entry 4u0y coloured by chain, side view.
PDB entry 4u0y coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.
Fillenberg SB, Grau FC, Seidel G, Muller YA
Nucleic Acids Res 43 1283-96 (2015)
PMID: 25564531

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118175 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
HTH-type transcriptional repressor NagR Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 78 amino acids
Theoretical weight: 8.97 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: O34817 (Residues: 1-75; Coverage: 31%)
Gene names: BSU35030, nagR, yvoA
Sequence domains: Bacterial regulatory proteins, gntR family
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P31
Unit cell:
a: 48.554Å b: 48.554Å c: 153.941Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.178 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era.
van der Heul et al. (2018)
3 more

2 mentions without citation

Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.
Fillenberg et al. (2015)
1 more