Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 27420.88 
• Atom Count: 1567 
• Residue Count: 222 
• Unique protein chains: 1

4FQE

KdgM porin

• DOI: 10.2210/pdb4FQE/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Dickeya dadantii (strain 3937)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-06-25 Released: 2013-06-26 
• Deposition Author(s): Hutter, C., Peneff, C.M., Wirth, C., Schirmer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 

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

• PubMed: 24914987 
• DOI: 10.1107/S1399004714007147
• Primary Citation of Related Structures:  
  4PR7


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Oligogalacturonate-specific porin kdgM	A	222	Dickeya dadantii (strain 3937)	Mutation(s): 0  Gene Names: kdgM
Find proteins for Q934G3 (Dickeya dadantii (strain 3937)) Go to UniProtKB:  Q934G3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OCT	A	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N
C8E	A	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 36.856	α = 90.00
b = 59.674	β = 106.80
c = 51.564	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	data scaling
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-25 
• Released Date: 2013-06-26 
• Deposition Author(s): Hutter, C., Peneff, C.M., Wirth, C., Schirmer, T.

Revision History 

• Version 1.0: 2013-06-26
  Type: Initial release
• Version 1.1: 2014-06-11
  Type: Database references
• Version 1.2: 2014-07-02
  Type: Database references
• Version 1.3: 2017-11-15
  Type: Refinement description