4BRB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic.

Li, D.Caffrey, M.

(2014) Sci.Rep. 4: 5806

  • DOI: 10.1038/srep05806
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane proteins play vital roles in the life of the cell and are important therapeutic targets. Producing them in large quantities, pure and fully functional is a major challenge. Many promising projects end when intractable aggregates or precipita ...

    Membrane proteins play vital roles in the life of the cell and are important therapeutic targets. Producing them in large quantities, pure and fully functional is a major challenge. Many promising projects end when intractable aggregates or precipitates form. Here we show how such unfolded aggregates can be solubilized and the solution mixed with lipid to spontaneously self-assemble a bicontinuous cubic mesophase into the bilayer of which the protein, in a confined, chaperonin-like environment, reconstitutes with 100% efficiency. The test protein, diacylglycerol kinase, reconstituted in the bilayer of the mesophase, was then crystallized in situ by the in meso or lipid cubic phase method providing an X-ray structure to a resolution of 2.55 Å. This highly efficient, inexpensive, simple and rapid approach should find application wherever properly folded, membrane reconstituted and functional proteins are required where the starting material is a denatured aggregate.


    Organizational Affiliation

    School of Biochemistry and Immunology & School of Medicine, Trinity College Dublin, Dublin, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIACYLGLYCEROL KINASE
A, B, C, D, E, F
130Escherichia coli (strain K12)Mutation(s): 7 
Gene Names: dgkA
EC: 2.7.1.107
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABN1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
78N
Query on 78N

Download SDF File 
Download CCD File 
A, B, C, D
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL (2R)
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.500α = 90.00
b = 91.570β = 90.00
c = 143.570γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-04 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Li, D., Caffrey, M.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-04-03
    Type: Data collection, Experimental preparation