› 4ihs

X-ray diffraction
3.1Å resolution

Crystal Structure of BenM_DBD/catB site 1 DNA Complex

Released:
DOI: 10.2210/pdb4ihs/pdb
PDB entry 4ihs coloured by chain, front view.
PDB entry 4ihs coloured by chain, side view.
PDB entry 4ihs coloured by chain, top view.
Source organism: Acinetobacter baylyi ADP1
Primary publication:
The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators.
Alanazi AM, Neidle EL, Momany C
Acta Crystallogr D Biol Crystallogr 69 1995-2007 (2013)
PMID: 24100318

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-117641 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HTH-type transcriptional regulator BenM Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 94 amino acids
Theoretical weight: 10.94 KDa
Source organism: Acinetobacter baylyi ADP1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68014 (Residues: 1-87; Coverage: 29%)
Gene names: ACIAD1435, benM, benR
Sequence domains: Bacterial regulatory helix-turn-helix protein, lysR family
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
catB site 1 DNA Chains: E, G
Molecule details ›
Chains: E, G
Length: 25 nucleotides
Theoretical weight: 7.64 KDa
Source organism: Acinetobacter baylyi ADP1
Expression system: Not provided
catB site 1 DNA - complement Chains: F, H
Molecule details ›
Chains: F, H
Length: 25 nucleotides
Theoretical weight: 7.71 KDa
Source organism: Acinetobacter baylyi ADP1
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MLI 2 x MLI
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P42212
Unit cell:
a: 156.493Å b: 156.493Å c: 141.525Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.178 0.203
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.
Dorman et al. (2016)
3 more

3 mentions without citation

Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures.
Housseini B Issa et al. (2018)
2 more