8X8G

Crystal structure of EndoSz mutant D234M, from Streptococcus equi subsp. Zooepidemicus Sz105, in complex with oligosaccharide G2S2-oxazoline

• PDB DOI: https://doi.org/10.2210/pdb8X8G/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus equi subsp. zooepidemicus Sz105
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-27 Released: 2024-07-03 
• Deposition Author(s): Guan, H.H., Lin, C.C., Hsieh, Y.C., Chen, C.J.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Literature

Structure-Based High-Efficiency Homogeneous Antibody Platform by Endoglycosidase Sz Provides Insights into Its Transglycosylation Mechanism

Hsieh, Y.C., Guan, H.H., Lin, C.C., Huang, T.Y., Chuankhayan, P., Chen, N.C., Wang, N.H., Hu, P.L., Tsai, Y.C., Huang, Y.C., Yoshimura, M., Lin, P.J., Hsieh, Y.H., Chen, C.J.

(2024) JACS Au 4: 2130-2150

• DOI: https://doi.org/10.1021/jacsau.4c00004

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 109.68 kDa 
• Atom Count: 7,334 
• Modelled Residue Count: 876 
• Deposited Residue Count: 961 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoside hydrolase	A	961	Streptococcus equi subsp. zooepidemicus Sz105	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose	B	9		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGO (Subject of Investigation/LOI)	C [auth A]	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE C8 H14 N O5 PDBSWNMXMILYCQ-PVFLNQBWSA-O
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002420	B	G2S2-oxazoline	Oligosaccharide /

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.061	α = 90
b = 232.603	β = 90
c = 50.654	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Guan, H.H., Lin, C.C., Hsieh, Y.C., Chen, C.J.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release