4D5B

Crystal structure of CymA from Klebsiella oxytoca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.1 of the entry. See complete history


Literature

Outer-membrane translocation of bulky small molecules by passive diffusion.

van den Berg, B.Prathyusha Bhamidimarri, S.Dahyabhai Prajapati, J.Kleinekathofer, U.Winterhalter, M.

(2015) Proc Natl Acad Sci U S A 112: E2991-E2999

  • DOI: https://doi.org/10.1073/pnas.1424835112
  • Primary Citation of Related Structures:  
    4D51, 4D5B, 4D5D, 4V3G, 4V3H

  • PubMed Abstract: 

    The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels. As a consequence, there is an "OM size-exclusion limit," and the uptake of bulky molecules with molecular masses of more than ∼ 600 Da is thought to be mediated by TonB-dependent, active transporters. Intriguingly, the OM protein CymA from Klebsiella oxytoca does not depend on TonB but nevertheless mediates efficient OM passage of cyclodextrins with diameters of up to ∼ 15 Å. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded β-barrel with a large pore that is occluded on the periplasmic side by the N-terminal 15 residues of the protein. Representing a previously unidentified paradigm in OM transport, CymA mediates the passive diffusion of bulky molecules via an elegant transport mechanism in which a mobile element formed by the N terminus acts as a ligand-expelled gate to preserve the permeability barrier of the OM.


  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom; bert.van-den-berg@ncl.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYMA
A, B
339Klebsiella oxytocaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q48391 (Klebsiella oxytoca)
Explore Q48391 
Go to UniProtKB:  Q48391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48391
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)
C, D, E, F
6N/A
Glycosylation Resources
GlyTouCan:  G22307HL
GlyCosmos:  G22307HL
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.559α = 90
b = 77.397β = 90
c = 110.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C8EClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2015-06-24
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Advisory, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary