9KAJ | pdb_00009kaj

Crystal Structure of Chalcone Syntase from Physcomitrella patens complexed with Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb9KAJ/pdb

• Classification: TRANSFERASE
• Organism(s): Physcomitrium patens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-10-28 Released: 2025-10-29 
• Deposition Author(s): Imaizumi, R., Waki, T., Yasuda, A., Yanai, T., Takeshita, K., Sakai, N., Yamamoto, M., Nakayama, T., Yamashita, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural basis, dynamics, and mode of action of enhancer of flavonoid production in metabolon

Imaizumi, R., Waki, T., Yasuda, A., Yanai, T., Takeshita, K., Sakai, N., Yamamoto, M., Nakayama, T., Yamashita, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 270.64 kDa 
• Atom Count: 18,034 
• Modeled Residue Count: 2,301 
• Deposited Residue Count: 2,478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone synthase	A, B, C, D, E, F	413	Physcomitrium patens	Mutation(s): 0  Gene Names: PHYPA_029015 EC: 2.3.1.74
UniProt
Find proteins for Q2VAZ3 (Physcomitrium patens) Explore Q2VAZ3  Go to UniProtKB:  Q2VAZ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	G [auth A], I [auth B], J [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
EDO	H [auth A], K [auth D], L [auth D], M [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B, C, D, E, F	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.17	α = 90
b = 198.99	β = 90
c = 68.43	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Imaizumi, R., Waki, T., Yasuda, A., Yanai, T., Takeshita, K., Sakai, N., Yamamoto, M., Nakayama, T., Yamashita, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H05470
Japan Society for the Promotion of Science (JSPS)	Japan	21H02115
Japan Society for the Promotion of Science (JSPS)	Japan	24K23286
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release