› 4zm0

X-ray diffraction
3.17Å resolution

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat

Released:
DOI: 10.2210/pdb4zm0/pdb
PDB entry 4zm0 coloured by chain, front view.
PDB entry 4zm0 coloured by chain, side view.
PDB entry 4zm0 coloured by chain, top view.
Source organism: Escherichia virus P1
Primary publication:
An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.
Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R
Nat Chem Biol 12 490-6 (2016)
PMID: 27159580

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118374 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Antitoxin phd Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 73 amino acids
Theoretical weight: 8.14 KDa
Source organism: Escherichia virus P1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q06253 (Residues: 1-73; Coverage: 100%)
Gene name: phd
Sequence domains: Antitoxin Phd_YefM, type II toxin-antitoxin system
Structure domains: YefM-like domain
DNA/RNA (5'-D(CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 14 nucleotides
Theoretical weight: 4.27 KDa
Source organism: Escherichia virus P1
Expression system: Not provided
DNA/RNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*A)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: Escherichia virus P1
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NA 1 x NA
Ligand 144 2 x 144
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P6122
Unit cell:
a: 165.98Å b: 165.98Å c: 156.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.223 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Formation, physiology, ecology, evolution and clinical importance of bacterial persisters.
Van den Bergh et al. (2017)
5 more