4D2E

Crystal structure of an integral membrane kinase - v2.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cell-Free Expression and in Meso Crystallisation of an Integral Membrane Kinase for Structure Determination.

Boland, C.Li, D.Shah, S.T.A.Haberstock, S.Dotsch, V.Bernhard, F.Caffrey, M.

(2014) Cell.Mol.Life Sci. 71: 4895

  • DOI: 10.1007/s00018-014-1655-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane proteins are key elements in cell physiology and drug targeting, but getting a high-resolution structure by crystallographic means is still enormously challenging. Novel strategies are in big demand to facilitate the structure determination ...

    Membrane proteins are key elements in cell physiology and drug targeting, but getting a high-resolution structure by crystallographic means is still enormously challenging. Novel strategies are in big demand to facilitate the structure determination process that will ultimately hasten the day when sequence information alone can provide a three-dimensional model. Cell-free or in vitro expression enables rapid access to large quantities of high-quality membrane proteins suitable for an array of applications. Despite its impressive efficiency, to date only two membrane proteins produced by the in vitro approach have yielded crystal structures. Here, we have analysed synergies of cell-free expression and crystallisation in lipid mesophases for generating an X-ray structure of the integral membrane enzyme diacylglycerol kinase to 2.28-Å resolution. The quality of cellular and cell-free-expressed kinase samples has been evaluated systematically by comparing (1) spectroscopic properties, (2) purity and oligomer formation, (3) lipid content and (4) functionality. DgkA is the first membrane enzyme crystallised based on cell-free expression. The study provides a basic standard for the crystallisation of cell-free-expressed membrane proteins and the methods detailed here should prove generally useful and contribute to accelerating the pace at which membrane protein structures are solved.


    Organizational Affiliation

    Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany.,Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

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

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

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Download CCD File 
D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
78N
Query on 78N

Download SDF File 
Download CCD File 
A, B, C, D, E
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL (2R)
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
 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: 2.28 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.290α = 90.00
b = 91.820β = 90.00
c = 143.920γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2019-02-27
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-10-09
    Type: Data collection, Derived calculations, Other