8IHW

X-ray crystal structure of D43R mutant of endo-1,4-beta glucanase from Eisenia fetida

• PDB DOI: https://doi.org/10.2210/pdb8IHW/pdb

• Classification: HYDROLASE
• Organism(s): Eisenia fetida
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2023-02-24 Released: 2023-12-06 
• Deposition Author(s): Kuroki, C., Hirano, Y., Nakazawa, M., Sakamoto, T., Tamada, T., Ueda, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.176 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

A single mutation Asp43Arg was increased 2.5-fold the catalytic activity and maintained the stability of cold-adapted endo-1,4-beta glucanase (Ef-EG2) from Eisenia fetida.

Kuroki, C., Hirano, Y., Nakazawa, M., Sakamoto, T., Tamada, T., Ueda, M.

(2023) Curr Res Biotechnol 5

• DOI: https://doi.org/10.1016/j.crbiot.2023.100126

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 51.9 kDa 
• Atom Count: 3,989 
• Modelled Residue Count: 433 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	462	Eisenia fetida	Mutation(s): 1  Gene Names: EF-EG2
UniProt
Find proteins for I2FI81 (Eisenia fetida) Explore I2FI81  Go to UniProtKB:  I2FI81

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.176 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.292	α = 90
b = 71.682	β = 114.233
c = 55.359	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Kuroki, C., Hirano, Y., Nakazawa, M., Sakamoto, T., Tamada, T., Ueda, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H03090

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release