4UP6 | pdb_00004up6

Crystal structure of the wild-type diacylglycerol kinase refolded in the lipid cubic phase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.371 (Depositor), 0.346 (DCC) 
  • R-Value Work: 
    0.325 (Depositor), 0.327 (DCC) 
  • R-Value Observed: 
    0.326 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: https://doi.org/10.1038/srep05806
  • Primary Citation Related Structures: 
    4BRB, 4UP6

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 42.76 kDa 
  • Atom Count: 2,472 
  • Modeled Residue Count: 323 
  • Deposited Residue Count: 390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DIACYLGLYCEROL KINASE
A, B, C
130Escherichia coli K-12Mutation(s): 0 
EC: 2.7.1.107
Membrane Entity: Yes 
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Explore P0ABN1 
Go to UniProtKB:  P0ABN1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABN1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.371 (Depositor), 0.346 (DCC) 
  • R-Value Work:  0.325 (Depositor), 0.327 (DCC) 
  • R-Value Observed: 0.326 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.39α = 90
b = 75.39β = 90
c = 197.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.2: 2019-04-03
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description