8IBL

MES bound form of PET-degrading cutinase Cut190 with thermostability-improving mutations of S226P/R228S/Q138A/D250C-E296C/Q123H/N202H and S176A inactivation

• PDB DOI: https://doi.org/10.2210/pdb8IBL/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomonospora viridis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-02-10 Released: 2023-03-15 
• Deposition Author(s): Emori, M., Numoto, N., Kamiya, N., Oda, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.263 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism.

Numoto, N., Kamiya, N., Oda, M.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.02.26.529345

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.32 kDa 
• Atom Count: 4,151 
• Modelled Residue Count: 524 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase family protein	A, B	263	Saccharomonospora viridis	Mutation(s): 8  Gene Names: Cut190, SAMN02982918_2340 EC: 3.1.1.74
UniProt
Find proteins for W0TJ64 (Saccharomonospora viridis) Explore W0TJ64  Go to UniProtKB:  W0TJ64

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES (Subject of Investigation/LOI)	D [auth A], G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.263 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.869	α = 90
b = 83.869	β = 90
c = 64.723	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Emori, M., Numoto, N., Kamiya, N., Oda, M.

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

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary