2WQ8 | pdb_00002wq8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.242 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Models: experimental
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This is version 1.5 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1021/ja2018477
  • Primary Citation of 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.

    • Organizational Affiliation: 

    School of Chemistry, University of Manchester, Manchester Interdisciplinary Biocentre, Manchester, M1 7DN, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GALACTOSE OXIDASE661Fusarium graminearumMutation(s): 9 
EC: 1.1.3.9
UniProt
Find proteins for P0CS93 (Gibberella zeae)
Explore P0CS93 
Go to UniProtKB:  P0CS93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CS93
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
O [auth A],
P [auth A],
Q [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU
Download Ideal Coordinates CCD File 
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY
Query on ACY
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
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), 0.220 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.464α = 90
b = 88.464β = 90
c = 410.846γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMACphasing
REFMACrefinement

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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