4D6I

Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 blood group A-tetrasaccharide (E558A L19 mutant)

• PDB DOI: https://doi.org/10.2210/pdb4D6I/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae SP3-BS71
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-11-11 Released: 2014-11-26 
• Deposition Author(s): Kwan, D.H., Constantinescu, I., Chapanian, R., Higgins, M.A., Samain, E., Boraston, A.B., Kizhakkedathu, J.N., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.206 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.87 kDa 
• Atom Count: 5,548 
• Modelled Residue Count: 587 
• Deposited Residue Count: 599 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSIDE HYDROLASE	A	599	Streptococcus pneumoniae SP3-BS71	Mutation(s): 4  EC: 3.2.1.102

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G66163TI GlyCosmos:  G66163TI GlyGen:  G66163TI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.206 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.3	α = 90
b = 154.48	β = 90
c = 97.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Kwan, D.H., Constantinescu, I., Chapanian, R., Higgins, M.A., Samain, E., Boraston, A.B., Kizhakkedathu, J.N., Withers, S.G.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references
• Version 1.2: 2015-05-20
  Changes: Database references
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary