1RMG

RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • DOI: 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) ...

    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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Studies of Rhamnogalacturonase a from Aspergillus Aculeatus
      Petersen, T.N., Christgau, S., Kofod, L.V., Kauppinen, S., Dalboge, H., Johnson, A.H., Larsen, S.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 105

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHAMNOGALACTURONASE AA422Aspergillus aculeatusMutation(s): 0 
Gene Names: rhgA
EC: 3.2.1 (PDB Primary Data), 3.2.1.171 (UniProt)
UniProt
Find proteins for Q00001 (Aspergillus aculeatus)
Explore Q00001 
Go to UniProtKB:  Q00001
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseB5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G51945PF
GlyCosmos:  G51945PF
GlyGen:  G51945PF
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
K [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
BMA (Subject of Investigation/LOI)
Query on BMA

Download Ideal Coordinates CCD File 
E [auth A], M [auth A], Q [auth A]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
D [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , L [auth A] , N [auth A] , 
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
 Ligand Interaction
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 = 62.9α = 90
b = 125.4β = 90
c = 137γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4-PROGRAMSdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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