1DXJ | pdb_00001dxj

Structure of the chitinase from jack bean

• PDB DOI: https://doi.org/10.2210/pdb1DXJ/pdb

• Classification: HYDROLASE
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 2000-01-10 Released: 2000-08-29 
• Deposition Author(s): Hahn, M., Hennig, M., Schlesier, B., Hohne, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure of Jack Bean Chitinase

Hahn, M., Hennig, M., Schlesier, B., Hohne, W.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1096

• PubMed: 10957628 
• DOI: https://doi.org/10.1107/s090744490000857x
• Primary Citation Related Structures: 
  1DXJ


• PubMed Abstract: 
  

  The structure of jack bean chitinase was solved at 1.8 A resolution by molecular replacement. It is an alpha-helical protein with three disulfide bridges. The active site is related in structure to animal and viral lysozymes. However, unlike in lysozyme, the architecture of the active site suggests a single-step cleavage. According to this mechanism, Glu68 is the proton donor and Glu90 assists in the reaction by moving towards the substrate and recruiting a water molecule that acts as the nucleophile. In this model, a water molecule was found in contact with Glu90 O(epsilon1) and Thr119 O(gamma) at a distance of 3.0 and 2.8 A, respectively. The model is in accordance with the observed inversion mechanism.

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Organizational Affiliation: 
• Institut für Biochemie, Charité, Humboldt-Universität, Monbijoustrasse 2, 10117 Berlin, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 26.24 kDa 
• Atom Count: 2,003 
• Modeled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS II CHITINASE	A	242	Canavalia ensiformis	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for O81934 (Canavalia ensiformis) Explore O81934  Go to UniProtKB:  O81934

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.69	α = 90
b = 67.69	β = 90
c = 110.21	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-29 
Deposition Author(s): Hahn, M., Hennig, M., Schlesier, B., Hohne, W.

Revision History  

• Version 1.0: 2000-08-29
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-06
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary