4JA4 | pdb_00004ja4

Inward open conformation of the xylose transporter XylE from E. coli

• PDB DOI: https://doi.org/10.2210/pdb4JA4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-02-18 Released: 2013-05-01 
• Deposition Author(s): Quistgaard, E.M., Low, C., Moberg, P., Tresaugues, L., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.318 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.288 (Depositor), 0.299 (DCC) 
• R-Value Observed: 
  0.290 (Depositor) 

Literature

Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.

Quistgaard, E.M., Low, C., Moberg, P., Tresaugues, L., Nordlund, P.

(2013) Nat Struct Mol Biol 20: 766-768

• PubMed: 23624861 
• DOI: https://doi.org/10.1038/nsmb.2569
• Primary Citation Related Structures: 
  4JA3, 4JA4


• PubMed Abstract: 
  

  Here we present two structures of the major facilitator (MFS) xylose transporter XylE from Escherichia coli in inward open and partially occluded inward open conformations. These structures provide key information about the transport cycle of XylE and the closely related human GLUT transporters. This is, to our knowledge, the first MFS transporter structure determined in more than one conformational state, which may establish XylE as an important MFS model protein.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 158.89 kDa 
• Atom Count: 10,130 
• Modeled Residue Count: 1,317 
• Deposited Residue Count: 1,455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-xylose-proton symporter	A, B, C	485	Escherichia coli K-12	Mutation(s): 0  Gene Names: xylE, b4031, JW3991 Membrane Entity: Yes
UniProt
Find proteins for P0AGF4 (Escherichia coli (strain K12)) Explore P0AGF4  Go to UniProtKB:  P0AGF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.318 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.288 (Depositor), 0.299 (DCC) 
• R-Value Observed: 0.290 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.82	α = 90
b = 125.82	β = 90
c = 380.68	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Quistgaard, E.M., Low, C., Moberg, P., Tresaugues, L., Nordlund, P.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations