› 6za3

X-ray diffraction
2.05Å resolution

Structure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in complex a palindromic DNA (C2221 space group)

Released:
DOI: 10.2210/pdb6za3/pdb
Model geometry
Fit model/data
PDB entry 6za3 coloured by chain, front view.
PDB entry 6za3 coloured by chain, side view.
PDB entry 6za3 coloured by chain, top view.
Source organism: Agrobacterium fabrum str. C58
Primary publication:
Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum.
Vigouroux A, Meyer T, Naretto A, Legrand P, Aumont-Nicaise M, Di Cicco A, Renoud S, Doré J, Lévy D, Vial L, Lavire C, Moréra S
OpenAccess logo Nucleic Acids Res 49 529-546 (2021)
PMID: 33313837

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-108917 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
HTH gntR-type domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 250 amino acids
Theoretical weight: 27.41 KDa
Source organism: Agrobacterium fabrum str. C58
Expression system: Escherichia coli
UniProt:
  • Canonical: A9CJ36 (Residues: 1-244; Coverage: 100%)
Gene name: Atu1419
Sequence domains:
DNA (5'-D(*AP*TP*GP*TP*AP*TP*AP*CP*AP*T)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Agrobacterium fabrum str. C58
Expression system: synthetic construct

Ligands and Environments

5 bound ligands:
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand EDO 2 x EDO
Ligand PG4 1 x PG4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2221
Unit cell:
a: 62.446Å b: 112.402Å c: 179.552Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.228
Expression systems:
  • Escherichia coli
  • synthetic construct

Quick links

Citations

3 citation in other articles

BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture.
Bandera et al. (2021)
2 more

1 mention without citation

Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum.
Vigouroux et al. (2021)