2WMG

Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 (Sp4GH98) in complex with the LewisY pentasaccharide blood group antigen.

• PDB DOI: https://doi.org/10.2210/pdb2WMG/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-06-30 Released: 2009-07-14 
• Deposition Author(s): Higgins, M.A., Whitworth, G.E., El Warry, N., Randriantsoa, M., Samain, E., Burke, R.D., Vocadlo, D.J., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 
• R-Value Observed: 0.160 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 67.45 kDa 
• Atom Count: 4,878 
• Modelled Residue Count: 553 
• Deposited Residue Count: 581 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOLECTIN-RELATED PROTEIN	A	581	Streptococcus pneumoniae TIGR4	Mutation(s): 1
UniProt
Find proteins for A0A0H2US34 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2US34  Go to UniProtKB:  A0A0H2US34

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G00052MO GlyCosmos:  G00052MO GlyGen:  G00052MO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900054	B	Lewis Y antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.86	α = 90
b = 90.87	β = 90
c = 116.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Higgins, M.A., Whitworth, G.E., El Warry, N., Randriantsoa, M., Samain, E., Burke, R.D., Vocadlo, D.J., Boraston, A.B.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary