1K7C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Molgaard, A.Larsen, S.

(2002) Acta Crystallogr.,Sect.D 58: 111-119

  • Also Cited By: 3C1U

  • 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 ...

    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.


    Related Citations: 
    • Rhamnogalacturonan acetylesterase, a member of the SGNH-hydrolase family.
      Molgaard, A.
      () TO BE PUBLISHED --: --
    • Molecular cloning and characterization of a rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
      Kauppinen, S.,Christgau, S.,Kofod, L.V.,Halkier, T.,Dorreich, K.,Dalboge, H.
      (1995) J.Biol.Chem. 270: 27172
    • Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
      Molgaard, A.,Kauppinen, S.,Larsen, S.
      (2000) Structure 8: 373
    • Crystallization and preliminary X-ray diffraction studies of the heterogeneously glycosylated enzyme rhamnogalacturonan acetylesterase from Aspergillus aculeatus.
      Molgaard, A.,Petersen, J.F.W.,Kauppinen, S.,Dalboge, H.,Johnsen, A.H.,Poulsen, J.-C.N.,Larsen, S.
      (1998) Acta Crystallogr.,Sect.D 54: 1026


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
rhamnogalacturonan acetylesterase
A
233Aspergillus aculeatusMutation(s): 0 
Gene Names: rha1
EC: 3.1.1.86
Find proteins for Q00017 (Aspergillus aculeatus)
Go to UniProtKB:  Q00017
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.170α = 90.00
b = 56.920β = 90.00
c = 71.690γ = 90.00
Software Package:
Software NamePurpose
MARdata reduction
SCALEPACKdata scaling
MLPHAREphasing
MARdata collection
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance