8JH8

Structure-based characterization and improvement of an enzymatic activity of Acremonium alcalophilum feruloyl esterase

• PDB DOI: https://doi.org/10.2210/pdb8JH8/pdb

• Classification: HYDROLASE
• Organism(s): Sodiomyces alcalophilus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-05-22 Released: 2024-04-17 
• Deposition Author(s): Phienluphon, A., Kondo, K., Mikami, B., Nagata, T., Katahira, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: in silico

Literature

Structure-Based Characterization and Improvement of an Enzymatic Activity of Acremonium alcalophilum Feruloyl Esterase

Phienluphon, A., Kondo, K., Mikami, B., Teo, K.S.K., Saito, K., Watanabe, T., Nagata, T., Katahira, M.

(2024) ACS Sustain Chem Eng 12: 3831-3840

• DOI: https://doi.org/10.1021/acssuschemeng.3c08222

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 27.55 kDa 
• Atom Count: 2,148 
• Modelled Residue Count: 242 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Feruloyl esterase	A	248	Sodiomyces alcalophilus	Mutation(s): 0  EC: 3.1.1.73
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.516	α = 90
b = 37.738	β = 125.928
c = 77.709	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Phienluphon, A., Kondo, K., Mikami, B., Nagata, T., Katahira, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H03192
Japan Society for the Promotion of Science (JSPS)	Japan	20K21477
Japan Society for the Promotion of Science (JSPS)	Japan	21H05519
Japan Society for the Promotion of Science (JSPS)	Japan	22H05596
Japan Society for the Promotion of Science (JSPS)	Japan	20K06524
Japan Society for the Promotion of Science (JSPS)	Japan	20K06164

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary