Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.28 kDa 
• Atom Count: 1842 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

1KS5

Structure of Aspergillus niger endoglucanase

• PDB DOI: 10.2210/pdb1KS5/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger
• Mutation(s): No 


• Deposited: 2002-01-10 Released: 2003-01-21 
• Deposition Author(s): Khademi, S., Zhang, D., Swanson, S.M., Wartenberg, A., Witte, C., Meyer, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.191 
• R-Value Work: 0.175 

Literature

Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.

Khademi, S., Zhang, D., Swanson, S.M., Wartenberg, A., Witte, K., Meyer, E.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 660-667

• PubMed: 11914491 
• DOI: 10.1107/s0907444902003360
• Primary Citation of Related Structures:  
  1KS4, 1KS5


• PubMed Abstract: 
  

The fungus Aspergillus niger is a main source of industrial cellulase. beta-1,4-Endoglucanase is the major component of cellulase from A. niger. In spite of widespread applications, little is known about the structure of this enzyme. Here, the structure of beta-1,4-endoglucanase from A. niger (EglA) was determined at 2.1 A resolution. Although there is a low sequence identity between EglA and CelB2, another member of family 12, the three-dimensional structures of their core regions are quite similar. The structural differences are mostly found in the loop regions, where CelB2 has an extra beta-sheet (beta-sheet C) at the non-reducing end of the binding cleft of the native enzyme. Incubation of EglA with PdCl(2) irreversibly inhibits the EglA activity. Structural studies of the enzyme-palladium complex show that three Pd(2+) ions bind to each EglA molecule. One of the Pd(2+) ions forms a coordinate covalent bond with Met118 S(delta) and the nucleophilic Glu116 O(epsilon1) at the active site of the enzyme. The other two Pd(2+) ions bind on the surface of the protein. Binding of Pd(2+) ions to EglA does not change the general conformation of the backbone of the protein significantly. Based on this structural study, one can conclude that the palladium ion directly binds to and blocks the active site of EglA and thus inactivates the enzyme.

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Organizational Affiliation: 

Biographics Laboratory, Texas A&M University, Department of Biochemistry and Biophysics, College Station, TX 77843-2128, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase A	A	223	Aspergillus niger	Mutation(s): 0  Gene Names: eglA, ATCC64974_2380, CAN33_0026800 EC: 3.2.1.4
UniProt
Find proteins for O74705 (Aspergillus niger) Explore O74705  Go to UniProtKB:  O74705

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.191 
• R-Value Work: 0.175 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.57	α = 90
b = 131.57	β = 90
c = 71.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-10 
• Released Date: 2003-01-21 
Deposition Author(s): Khademi, S., Zhang, D., Swanson, S.M., Wartenberg, A., Witte, C., Meyer, E.F.

Revision History  

• Version 1.0: 2003-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary