2WQ8 | pdb_00002wq8

Glycan labelling using engineered variants of galactose oxidase obtained by directed evolution

• PDB DOI: https://doi.org/10.2210/pdb2WQ8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium graminearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-08-14 Released: 2010-09-01 
• Deposition Author(s): Rannes, J.G., Ioannou, A., Willies, S.C., Behrens, C., Grogan, G.J., Flitsch, S.L., Turner, N.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.242 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Models: experimental

Literature

Glycoprotein Labeling Using Engineered Variants of Galactose Oxidase Obtained by Directed Evolution.

Rannes, J.B., Ioannou, A., Willies, S.C., Grogan, G., Behrens, C., Flitsch, S.L., Turner, N.J.

(2011) J Am Chem Soc 133: 8436

• PubMed: 21526835 
• DOI: https://doi.org/10.1021/ja2018477
• Primary Citation Related Structures: 
  2WQ8


• PubMed Abstract: 
  

  A directed evolution approach has been used for the generation of variants of galactose oxidase (GOase) that can selectively oxidize glycans on glycoproteins. The aldehyde function introduced on the glycans D-mannose (Man) and D-N-acetyl glucosamine (GlcNAc) by the enzyme variants could then be used to label the glycoproteins and also whole cells that display mannosides on their surface.

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Organizational Affiliation: 
• School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.25 kDa 
• Atom Count: 5,278 
• Modeled Residue Count: 639 
• Deposited Residue Count: 661 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GALACTOSE OXIDASE	A	661	Fusarium graminearum	Mutation(s): 9  EC: 1.1.3.9
UniProt
Find proteins for P0CS93 (Gibberella zeae) Explore P0CS93  Go to UniProtKB:  P0CS93

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.242 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.464	α = 90
b = 88.464	β = 90
c = 410.846	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Rannes, J.G., Ioannou, A., Willies, S.C., Behrens, C., Grogan, G.J., Flitsch, S.L., Turner, N.J.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-06-09
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-30
  Changes: Advisory, Data collection, Derived calculations, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary