2IQ7

Crystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins

• PDB DOI: https://doi.org/10.2210/pdb2IQ7/pdb

• Classification: HYDROLASE
• Organism(s): Colletotrichum lupini
• Mutation(s): No 


• Deposited: 2006-10-13 Released: 2007-10-23 
• Deposition Author(s): Bonivento, D., Federici, L., Matteo, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.196 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Macromolecule Content

• Total Structure Weight: 244.66 kDa 
• Atom Count: 19,675 
• Modelled Residue Count: 2,372 
• Deposited Residue Count: 2,373 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endopolygalacturonase	A, B, C, D, E, F, G	339	Colletotrichum lupini	Mutation(s): 0  EC: 3.2.1.15
UniProt
Find proteins for A1E266 (Colletotrichum lupini var. setosum) Explore A1E266  Go to UniProtKB:  A1E266

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79306TC GlyCosmos:  G79306TC GlyGen:  G79306TC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J [auth L], K [auth M], L [auth N], M [auth O], N [auth Q]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	O [auth A], P [auth B], S [auth C], T [auth D], U [auth E], W [auth F]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	Q [auth B], V [auth E], X [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	R [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.196 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.64	α = 90
b = 127.266	β = 90
c = 205.828	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Bonivento, D., Federici, L., Matteo, A.D.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary