› 5ed4

X-ray diffraction
2.4Å resolution

Structure of a PhoP-DNA complex

Released:
DOI: 10.2210/pdb5ed4/pdb
PDB entry 5ed4 coloured by chain, front view.
PDB entry 5ed4 coloured by chain, side view.
PDB entry 5ed4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis.
He X, Wang L, Wang S
Sci Rep 6 24442 (2016)
PMID: 27079268

Function and Biology Details

Reaction catalysed: 
A phosphate monoester + H(2)O = an alcohol + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118624 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Possible two component system response transcriptional positive regulator PhoP Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 250 amino acids
Theoretical weight: 27.85 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P71814 (Residues: 1-247; Coverage: 100%)
Gene names: Rv0757, phoP
Sequence domains:
Structure domains:
DNA (26-MER) Chains: C, G
Molecule details ›
Chains: C, G
Length: 26 nucleotides
Theoretical weight: 7.93 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (26-MER) Chains: D, H
Molecule details ›
Chains: D, H
Length: 26 nucleotides
Theoretical weight: 8.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 6 x CA
Ligand EDO 4 x EDO
Ligand CAC 1 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 92.24Å b: 98.176Å c: 167.888Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

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

7 mentions without citation

The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development.
Yan et al. (2022)
6 more