8Y64 | pdb_00008y64

Crystal structure of open state ferulic acid decarboxylase from Saccharomyces cerevisiae, F397V/I398L/T438P/P441V mutant

• PDB DOI: https://doi.org/10.2210/pdb8Y64/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-02-01 Released: 2025-01-01 
• Deposition Author(s): Feng, Y.B., Song, X., Zhu, X.N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Integrated strategies for engineering ferulic acid decarboxylase with tunnel conformation and substrate pocket for adapting non-natural substrates.

Zhu, X.N., Feng, Y.B., Wang, M.D., Li, S., Li, H.F., Liu, L., Xue, S.

(2025) Biochem Eng J 213

• DOI: https://doi.org/10.1016/j.bej.2024.109566

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.02 kDa 
• Atom Count: 8,977 
• Modeled Residue Count: 1,004 
• Deposited Residue Count: 1,006 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferulic acid decarboxylase 1	A, B	503	Saccharomyces cerevisiae	Mutation(s): 4  Gene Names: FDC1, YDR539W, D3703.2 EC: 4.1.1.102
UniProt
Find proteins for Q03034 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03034  Go to UniProtKB:  Q03034

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.778	α = 90
b = 81.83	β = 90
c = 166.321	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Feng, Y.B., Song, X., Zhu, X.N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release