8IHW | pdb_00008ihw

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.176 (Depositor), 0.177 (DCC)
R-Value Work:
0.144 (Depositor), 0.145 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	462	Eisenia fetida	Mutation(s): 1 Gene Names: EF-EG2 EC: 3.2.1.4
UniProt
Find proteins for I2FI81 (Eisenia fetida) Explore I2FI81 Go to UniProtKB: I2FI81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I2FI81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.176 (Depositor), 0.177 (DCC)
R-Value Work: 0.144 (Depositor), 0.145 (DCC)
R-Value Observed: 0.145 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release
Version 1.1: 2024-11-20
Changes: Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.