› 3w6v

X-ray diffraction
2.95Å resolution

Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA

Released:
DOI: 10.2210/pdb3w6v/pdb
PDB entry 3w6v coloured by chain, front view.
PDB entry 3w6v coloured by chain, side view.
PDB entry 3w6v coloured by chain, top view.
Source organism: Streptomyces griseus
Primary publication:
Complex structure of the DNA-binding domain of AdpA, the global transcription factor in Streptomyces griseus, and a target duplex DNA reveals the structural basis of its tolerant DNA sequence specificity.
Yao MD, Ohtsuka J, Nagata K, Miyazono K, Zhi Y, Ohnishi Y, Tanokura M
J Biol Chem 288 31019-29 (2013)
PMID: 24019524

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117070 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HTH araC/xylS-type domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 147 amino acids
Theoretical weight: 16.74 KDa
Source organism: Streptomyces griseus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9S166 (Residues: 215-340; Coverage: 31%)
Gene names: NCTC13033_02525, adpA, rhaS_1
Sequence domains: Helix-turn-helix domain
Structure domains: Homeodomain-like
DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.83 KDa
Source organism: Streptomyces griseus
Expression system: Not provided
DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.97 KDa
Source organism: Streptomyces griseus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: C2221
Unit cell:
a: 76.51Å b: 100.64Å c: 100.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.236 0.278
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 citation in other articles

Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism.
Guyet et al. (2014)
9 more

5 mentions without citation

Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa.
Zhao et al. (2016)
4 more