1RMG

RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS

• PDB DOI: https://doi.org/10.2210/pdb1RMG/pdb

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


• Deposited: 1997-02-26 Released: 1998-03-04 
• Deposition Author(s): Petersen, T.N., Kauppinen, S., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.

Petersen, T.N., Kauppinen, S., Larsen, S.

(1997) Structure 5: 533-544

• PubMed: 9115442 
• DOI: https://doi.org/10.1016/s0969-2126(97)00209-8
• Primary Citation of Related Structures:  
  1RMG


• PubMed Abstract: 
  

  Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l.

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Organizational Affiliation: 

Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.93 kDa 
• Atom Count: 3,576 
• Modelled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHAMNOGALACTURONASE A	A	422	Aspergillus aculeatus	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for Q00001 (Aspergillus aculeatus) Explore Q00001  Go to UniProtKB:  Q00001

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[beta-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	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51945PF GlyCosmos:  G51945PF GlyGen:  G51945PF

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	K [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
BMA	E [auth A], M [auth A], Q [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	D [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth A], N [auth A], O [auth A], P [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.214 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.9	α = 90
b = 125.4	β = 90
c = 137	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
CCP4-PROGRAMS	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-04 
Deposition Author(s): Petersen, T.N., Kauppinen, S., Larsen, S.

Revision History  

• Version 1.0: 1998-03-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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: Atomic model, Data collection, Derived calculations, Structure summary