Structure of E.coli rhomboid protease GlpG active site mutant, S201T in trigonal crystal form

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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This is version 1.5 of the entry. See complete history


Structure of Rhomboid Protease in a Lipid Environment

Vinothkumar, K.R.

(2011) J Mol Biol 407: 232

  • DOI: https://doi.org/10.1016/j.jmb.2011.01.029
  • Primary Citation of Related Structures:  
    2XTU, 2XTV

  • PubMed Abstract: 

    Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer, yet all the structures determined thus far are in a nonnative detergent environment. There remains a possibility of structural artefacts arising from the use of detergents. In an attempt to address the effect of detergents on the structure of rhomboid protease, crystals of GlpG, an Escherichia coli rhomboid protease in a lipid environment, were obtained using two alternative approaches. The structure of GlpG refined to 1. 7-Å resolution was obtained from crystals grown in the presence of lipid bicelles. This structure reveals well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of protein and arrange such that they match the hydrophobic thickness of GlpG. Virtually identical two-dimensional crystals were also obtained after detergent removal by dialysis. A comparison of an equivalent structure determined in a completely delipidated detergent environment provides insights on how detergent substitutes for lipid. A detergent molecule is also observed close to the active site, helping to postulate a model for substrate binding and hydrolysis in rhomboids.

  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. vkumar@mrc-lmb.cam.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RHOMBOID PROTEASE GLPG181Escherichia coli BL21(DE3)Mutation(s): 1 
Membrane Entity: Yes 
Find proteins for P09391 (Escherichia coli (strain K12))
Explore P09391 
Go to UniProtKB:  P09391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09391
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BNG

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
nonyl beta-D-glucopyranoside
C15 H30 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.25α = 90
b = 110.25β = 90
c = 127.6γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-02-27
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary