Rhamnogalacturonan acetylesterase with seven N-linked carbohydrate residues distributed at two N-glycosylation sites refined at 1.12 A resolution

Experimental Data Snapshot

  • Resolution: 1.12 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 

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A branched N-linked glycan at atomic resolution in the 1.12 A structure of rhamnogalacturonan acetylesterase.

Molgaard, A.Larsen, S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 111-119

  • DOI: https://doi.org/10.1107/s0907444901018479
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the glycoprotein rhamnogalacturonan acetylesterase from Aspergillus aculeatus has been refined to a resolution of 1.12 A using synchrotron data collected at 263 K. Both of the two putative N-glycosylation sites at Asn104 and Asn182 are glycosylated and, owing to crystal contacts, the glycan structure at Asn182 is exceptionally well defined in the electron-density maps, showing the six-carbohydrate structure Manalpha1-6(Manalpha1-3)Manalpha1-6Manbeta1-4GlcNAcbeta1-4GlcNAcbeta-Asn182. Equivalent carbohydrate residues were restrained to have similar geometries, but were refined without target values. The refined bond lengths and angles were compared with the values obtained from small-molecule studies that form the basis for the dictionaries used for glycoprotein refinement.

  • Organizational Affiliation

    Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rhamnogalacturonan acetylesterase233Aspergillus aculeatusMutation(s): 0 
Find proteins for Q00017 (Aspergillus aculeatus)
Explore Q00017 
Go to UniProtKB:  Q00017
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00017
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G17987PO
GlyCosmos:  G17987PO
GlyGen:  G17987PO
Experimental Data & Validation

Experimental Data

  • Resolution: 1.12 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.103 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.17α = 90
b = 56.92β = 90
c = 71.69γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary