Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54667.85 
• Atom Count: 3885 
• Residue Count: 508 
• Unique protein chains: 1

1NKG

Rhamnogalacturonan lyase from Aspergillus aculeatus

• DOI: 10.2210/pdb1NKG/pdb

• Classification: LYASE
• Organism(s): Aspergillus aculeatus
• Expression System: Aspergillus oryzae


• Deposited: 2003-01-03 Released: 2004-05-25 
• Deposition Author(s): McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 

Literature

Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4.

McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

(2004) Febs Lett. 565: 188-194

• PubMed: 15135077 
• DOI: 10.1016/j.febslet.2004.03.094


• PubMed Abstract: 
  

Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from Aspergillus aculeatus has been determined to 1.5 A resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows structural homology to non-catalytic domains from other carbohydrate active enzymes.

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Related Citations: 

• A stepwise optimization of crystals of rhamnogalacturonan lyase from Aspergillus aculeatus
  Kadirvelraj, R.,Harris, P.,Poulsen, J.-C.N.,Kauppinen, S.,Larsen, S.
  (2002) Acta Crystallogr.,Sect.D 58: 1346




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Organizational Affiliation: 

Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, DK, Denmark. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Rhamnogalacturonase B	A	508	Aspergillus aculeatus	Mutation(s): 0  Gene Names: rglA (RGL4) EC: 4.2.2.23
Find proteins for Q00019 (Aspergillus aculeatus) Go to UniProtKB:  Q00019

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 77.009	α = 90.00
b = 77.009	β = 90.00
c = 170.787	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
RESOLVE	phasing
SOLVE	phasing
CNS	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-03 
• Released Date: 2004-05-25 
• Deposition Author(s): McDonough, M.A., Kadirvelraj, R., Harris, P., Poulsen, J.C., Larsen, S.

Revision History 

• Version 1.0: 2004-05-25
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2018-01-24
  Type: Database references