4PR7

KdgM porin in complex with disordered oligogalacturonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the oligogalacturonate-specific KdgM porin.

Hutter, C.A.Lehner, R.Wirth, C.h.Condemine, G.Peneff, C.Schirmer, T.

(2014) Acta Crystallogr.,Sect.D 70: 1770-1778

  • DOI: 10.1107/S1399004714007147
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The phytopathogenic Gram-negative bacterium Dickeya dadantii (Erwinia chrysanthemi) feeds on plant cell walls by secreting pectinases and utilizing the oligogalacturanate products. An outer membrane porin, KdgM, is indispensable for the uptake of the ...

    The phytopathogenic Gram-negative bacterium Dickeya dadantii (Erwinia chrysanthemi) feeds on plant cell walls by secreting pectinases and utilizing the oligogalacturanate products. An outer membrane porin, KdgM, is indispensable for the uptake of these acidic oligosaccharides. Here, the crystal structure of KdgM determined to 1.9 Å resolution is presented. KdgM is folded into a regular 12-stranded antiparallel β-barrel with a circular cross-section defining a transmembrane pore with a minimal radius of 3.1 Å. Most of the loops that would face the cell exterior in vivo are disordered, but nevertheless mediate contact between densely packed membrane-like layers in the crystal. The channel is lined by two tracks of arginine residues facing each other across the pore, a feature that is conserved within the KdgM family and is likely to facilitate the diffusion of acidic oligosaccharides.


    Organizational Affiliation

    Focal Area of Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligogalacturonate-specific porin KdgM
A
222Dickeya dadantii (strain 3937)Mutation(s): 0 
Gene Names: kdgM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
KdgM *monomeric* porin in complex with disordered oligogalacturonate
Find proteins for Q934G3 (Dickeya dadantii (strain 3937))
Go to UniProtKB:  Q934G3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download SDF File 
Download CCD File 
A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
C8E
Query on C8E

Download SDF File 
Download CCD File 
A
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
ADA
Query on ADA

Download SDF File 
Download CCD File 
A
ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.857α = 90.00
b = 59.731β = 106.54
c = 51.596γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references