8ZIL | pdb_00008zil

Gamma-lyase CndF in complex with ethyl acetoacetate

• PDB DOI: https://doi.org/10.2210/pdb8ZIL/pdb

• Classification: LYASE
• Organism(s): Penicillium citrinum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-14 Released: 2025-11-19 
• Deposition Author(s): Gao, Y., Zhou, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanism of the Pyridoxal 5'-Phosphate-Dependent Amino Acid gamma-Substitution Enzyme in 6-Alkyl-Pipecolate Biosynthesis

Gao, Y., Wang, B., Zhou, J., Gu, Y.

(2025) ACS Catal : 18893-18907

• DOI: https://doi.org/10.1021/acscatal.5c04786

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: 126.42 kDa 
• Atom Count: 7,452 
• Modeled Residue Count: 945 
• Deposited Residue Count: 1,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLP dependent gamma-lyase CndF	A, B	568	Penicillium citrinum	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EAC (Subject of Investigation/LOI)	D [auth A]	ethyl 3-oxobutanoate C6 H10 O3 XYIBRDXRRQCHLP-UHFFFAOYSA-N
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.842	α = 90
b = 101.768	β = 90
c = 127.985	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: 2025-11-19 
Deposition Author(s): Gao, Y., Zhou, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release
  
• Version 1.1: 2025-11-26
  Changes: Database references