2WVP

Synthetically modified OmpG

• PDB DOI: https://doi.org/10.2210/pdb2WVP/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2009-10-19 Released: 2010-07-14 
• Deposition Author(s): Grosse, W., Reiss, P., Reitz, S., Cebi, M., Luebben, W., Koert, U., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.287 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

Structural and Functional Characterization of a Synthetically Modified Ompg.

Grosse, W., Reiss, P., Reitz, S., Cebi, M., Luebben, W., Koert, U., Essen, L.-O.

(2010) Bioorg Med Chem 18: 7716

• PubMed: 20378361 
• DOI: https://doi.org/10.1016/j.bmc.2010.03.044
• Primary Citation of Related Structures:  
  2WVP


• PubMed Abstract: 
  

  Chemical modification of ion channels has recently attracted attention due to their potential use in stochastic sensing and neurobiology. Among the available channel templates stable β-barrel proteins have shown their potential for large scale chemical modifications due to their wide pore lumen. Ion-channel hybrids using the outer membrane protein OmpG were generated by S-alkylation with a synthetic modulator and functionally as well as structurally characterized. The dansyl moiety of the used modulator resulted in partial blockage of current though the OmpG channel with its gating characteristics mainly unaffected. The crystal structure of an OmpG-dansyl hybrid at 2.4Å resolution correlates this finding by showing that the modulator lines the inner walling of the OmpG pore. These results underline the suitability of OmpG as a structural base for the construction of stochastic sensors.

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Organizational Affiliation: 

Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Straße, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.94 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 262 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OUTER MEMBRANE PROTEIN G	A	286	Escherichia coli K-12	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for P76045 (Escherichia coli (strain K12)) Explore P76045  Go to UniProtKB:  P76045

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
420	B [auth A]	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE C16 H20 I N3 O3 S QDHGMMDEGVINBU-UHFFFAOYSA-N
C8E	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.287 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.56	α = 90
b = 69.81	β = 103.6
c = 59.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Grosse, W., Reiss, P., Reitz, S., Cebi, M., Luebben, W., Koert, U., Essen, L.-O.

Revision History  

• Version 1.0: 2010-07-14
  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: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description