1DEX

RHAMNOGALACTURONAN ACETYLESTERASE FROM ASPERGILLUS ACULEATUS AT 1.9 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1DEX/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus aculeatus
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 1999-11-16 Released: 2000-04-26 
• Deposition Author(s): Molgaard, A., Kauppinen, S., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.162 

Literature

Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.

Molgaard, A., Kauppinen, S., Larsen, S.

(2000) Structure 8: 373-383

• PubMed: 10801485 
• DOI: https://doi.org/10.1016/s0969-2126(00)00118-0
• Primary Citation of Related Structures:  
  1DEO, 1DEX


• PubMed Abstract: 
  

  The complex polysaccharide rhamnogalacturonan constitutes a major part of the hairy region of pectin. It can have different types of carbohydrate sidechains attached to the rhamnose residues in the backbone of alternating rhamnose and galacturonic acid residues; the galacturonic acid residues can be methylated or acetylated. Aspergillus aculeatus produces enzymes that are able to perform a synergistic degradation of rhamnogalacturonan. The deacetylation of the backbone by rhamnogalacturonan acetylesterase (RGAE) is an essential prerequisite for the subsequent action of the enzymes that cleave the glycosidic bonds.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.92 kDa 
• Atom Count: 1,923 
• Modelled Residue Count: 233 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHAMNOGALACTURONAN ACETYLESTERASE	A	233	Aspergillus aculeatus	Mutation(s): 0
UniProt
Find proteins for Q00017 (Aspergillus aculeatus) Explore Q00017  Go to UniProtKB:  Q00017

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G94106MV GlyCosmos:  G94106MV GlyGen:  G94106MV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 57.08	β = 90
c = 71.86	γ = 90

Software Package:

Software Name	Purpose
ROTAVATA	data reduction
MLPHARE	phasing
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-26 
Deposition Author(s): Molgaard, A., Kauppinen, S., Larsen, S.

Revision History  

• Version 1.0: 2000-04-26
  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 1.3: 2017-10-04
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary