1KCC

Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb1KCC/pdb

• Classification: HYDROLASE
• Organism(s): Chondrostereum purpureum
• Mutation(s): No 


• Deposited: 2001-11-08 Released: 2002-06-05 
• Deposition Author(s): Shimizu, T., Nakatsu, T., Miyairi, K., Okuno, T., Kato, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.136 
• R-Value Work: 0.109 
• R-Value Observed: 0.114 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.35 kDa 
• Atom Count: 3,130 
• Modelled Residue Count: 333 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOPOLYGALACTURONASE	A	335	Chondrostereum purpureum	Mutation(s): 0  EC: 3.2.1.15
UniProt
Find proteins for P79074 (Chondrostereum purpureum) Explore P79074  Go to UniProtKB:  P79074

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GTR	B [auth A]	beta-D-galactopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-DTEWXJGMSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.136 
• R-Value Work: 0.109 
• R-Value Observed: 0.114 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.515	α = 72.31
b = 52.138	β = 69.09
c = 37.187	γ = 70.35

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
SHELXL-97	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-05 
Deposition Author(s): Shimizu, T., Nakatsu, T., Miyairi, K., Okuno, T., Kato, H.

Revision History  

• Version 1.0: 2002-06-05
  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: 2015-10-14
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary