4XXJ

Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin.

Bratanov, D.Balandin, T.Round, E.Shevchenko, V.Gushchin, I.Polovinkin, V.Borshchevskiy, V.Gordeliy, V.

(2015) PLoS One 10: e0128390-e0128390

  • DOI: https://doi.org/10.1371/journal.pone.0128390
  • Primary Citation of Related Structures:  
    4XXJ

  • PubMed Abstract: 

    Heterologous overexpression of functional membrane proteins is a major bottleneck of structural biology. Bacteriorhodopsin from Halobium salinarum (bR) is a striking example of the difficulties in membrane protein overexpression. We suggest a general approach with a finite number of steps which allows one to localize the underlying problem of poor expression of a membrane protein using bR as an example. Our approach is based on constructing chimeric proteins comprising parts of a protein of interest and complementary parts of a homologous protein demonstrating advantageous expression. This complementary protein approach allowed us to increase bR expression by two orders of magnitude through the introduction of two silent mutations into bR coding DNA. For the first time the high quality crystals of bR expressed in E. Coli were obtained using the produced protein. The crystals obtained with in meso nanovolume crystallization diffracted to 1.67 Å.


  • Organizational Affiliation

    Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany; Institute of Crystallography, University of Aachen (RWTH), Jägerstrasse 17-19, Aachen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin
A, B, C
269Halobacterium salinarumMutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPG
Query on MPG

Download Ideal Coordinates CCD File 
MA [auth C],
Q [auth A],
Z [auth B]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
D [auth A]
DA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LYR
Query on LYR
A, B, C
L-PEPTIDE LINKINGC26 H42 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.84α = 90
b = 60.76β = 99.78
c = 113.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description