1UKR | pdb_00001ukr

STRUCTURE OF ENDO-1,4-BETA-XYLANASE C

• PDB DOI: https://doi.org/10.2210/pdb1UKR/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-08-23 Released: 1997-12-24 
• Deposition Author(s): Krengel, U., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.179 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.

Krengel, U., Dijkstra, B.W.

(1996) J Mol Biology 263: 70-78

• PubMed: 8890913 
• DOI: https://doi.org/10.1006/jmbi.1996.0556
• Primary Citation Related Structures: 
  1UKR


• PubMed Abstract: 
  

  The crystal structure of endo-1,4-beta-xylanase I from Aspergillus niger has been solved by molecular replacement and was refined to 2.4 A resolution. The final R-factor for all data from 6 to 2.4 A is 17.9%. The A. niger xylanase has a characteristic fold which is unique for family G xylanases (root-mean-square deviation = 1.1 A to Trichoderma reesei xylanase I, which has 53% sequence identity). It consists of a single domain composed predominantly of beta-strands. Two beta-sheets are twisted around a deep, long cleft, which is lined with many aromatic amino acid residues and is large enough to accommodate at least four xylose residues. The two conserved glutamate residues, Glu79 and Glu170, which are likely to be involved in catalysis, reach into this cleft from opposite sides. A niger xylanase I is of particular commercial interest because of its low pH optimum. A model is proposed which explains this low pH optimum compared to other members of xylanase family G.

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Organizational Affiliation: 
• BIOSON Research Institute, University of Groningen, The Netherlands.

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.

Macromolecule Content 

• Total Structure Weight: 79.42 kDa 
• Atom Count: 5,840 
• Modeled Residue Count: 724 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-B-XYLANASE I	A, B, C, D	184	Aspergillus niger	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P55329 (Aspergillus niger) Explore P55329  Go to UniProtKB:  P55329

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.179 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.3	α = 90
b = 85.3	β = 90
c = 113.8	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
BRUTE	model building
X-PLOR	refinement
XDS	data reduction
BRUTE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-24 
Deposition Author(s): Krengel, U., Dijkstra, B.W.

Revision History  

• Version 1.0: 1997-12-24
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary