4M1U

The crystal structure of Stx2 and a disaccharide ligand

• PDB DOI: https://doi.org/10.2210/pdb4M1U/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O157:H7, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-04 Released: 2013-11-20 
• Deposition Author(s): Yin, J., James, M.N.G., Jacobson, J.M., Kitov, P.I., Bundle, D.R., Mulvey, G., Armstrong, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 73.75 kDa 
• Atom Count: 5,796 
• Modelled Residue Count: 631 
• Deposited Residue Count: 647 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga toxin 2 A-subunit	A	297	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: ECs1205, stx 2 A-subunit, stx2 A-subunit, stx2A, Z1464 EC: 3.2.2.22
UniProt
Find proteins for Q7DI68 (Escherichia coli O157:H7) Explore Q7DI68  Go to UniProtKB:  Q7DI68

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga toxin 2 B subunit	B, C, D, E, F	70	Escherichia coli	Mutation(s): 0  Gene Names: stx2B, stx2dB, stx2vB, stxB2, stxII, vtx2B
UniProt
Find proteins for Q7DJJ2 (Escherichia coli) Explore Q7DJJ2  Go to UniProtKB:  Q7DJJ2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-methyl beta-D-galactopyranoside	G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G78497LG GlyCosmos:  G78497LG

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	I [auth B], J [auth C], K [auth D]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.25	α = 90
b = 146.25	β = 90
c = 60.31	γ = 120

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Yin, J., James, M.N.G., Jacobson, J.M., Kitov, P.I., Bundle, D.R., Mulvey, G., Armstrong, G.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references
• Version 1.2: 2014-02-19
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary