› 4brb

X-ray diffraction
2.55Å resolution

Crystal structure of the integral membrane enzyme DgkA-ref, delta 7

Released:
DOI: 10.2210/pdb4brb/pdb
PDB entry 4brb coloured by chain, front view.
PDB entry 4brb coloured by chain, side view.
PDB entry 4brb coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Renaturing membrane proteins in the lipid cubic phase, a nanoporous membrane mimetic.
Li D, Caffrey M
Sci Rep 4 5806 (2014)
PMID: 25055873

Function and Biology Details

Reaction catalysed: 
ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142184 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diacylglycerol kinase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 130 amino acids
Theoretical weight: 14.2 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABN1 (Residues: 2-122; Coverage: 99%)
Gene names: JW4002, b4042, dgk, dgkA
Sequence domains: Prokaryotic diacylglycerol kinase
Structure domains: Helix Hairpins

Ligands and Environments

4 bound ligands:
Ligand 78N 10 x 78N
Ligand ZN 1 x ZN
Ligand FLC 1 x FLC
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 75.5Å b: 91.57Å c: 143.57Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.217 0.261
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry.
Bolla et al. (2019)
1 more

2 mentions without citation

A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.
Caffrey M. (2015)
1 more