9ILO | pdb_00009ilo

Crystal structure of CTB10-M4

• PDB DOI: https://doi.org/10.2210/pdb9ILO/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Cercospora sp. JNU001
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-01 Released: 2025-05-14 
• Deposition Author(s): Fu, K., Rao, Y.J.
• Funding Organization(s): Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.220 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Light-Driven Deracemization by a Designed Photoenzyme.

Li, M., Zhang, Y., Fu, K., Deng, Z., Yuan, Z., Luo, Z., Rao, Y.

(2025) J Am Chem Soc 147: 13190-13199

• PubMed: 40219972 
• DOI: https://doi.org/10.1021/jacs.4c16521
• Primary Citation Related Structures: 
  9IKU, 9ILO, 9IM9, 9IPR


• PubMed Abstract: 
  

  The creation of enzymes with abiological abilities offers exciting opportunities to access new-to-nature biocatalysis beyond that found in nature. Here, we repurpose a novel protein scaffold, CTB10, as an artificial photoenzyme through genetic code expansion. It enables catalytic deracemization of cyclopropane, a process that remains inaccessible to traditional biocatalysis due to its thermodynamically unfavorable nature. Following structural optimization through directed evolution, a broad substrate scope with high enantioselectivities is achieved. Furthermore, the crystal structure of the CTB10-based photoenzyme-substrate complex well demonstrates how the catalytic chiral cavity is sculpted to promote efficient and selective light-enabled deracemization. Therefore, this study unlocks the potential for achieving challenging deracemization through biocatalysis.

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Organizational Affiliation: 
• Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China.
School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, P. R. China.

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: homology

Macromolecule Content 

• Total Structure Weight: 32.9 kDa 
• Atom Count: 2,219 
• Modeled Residue Count: 249 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTB10	A, B	141	Cercospora sp. JNU001	Mutation(s): 5  EC: 1
UniProt
Find proteins for A0A2G5I8P4 (Cercospora beticola) Explore A0A2G5I8P4  Go to UniProtKB:  A0A2G5I8P4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PBF	A, B	L-PEPTIDE LINKING	C16 H15 N O3		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.220 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.181	α = 90
b = 121.186	β = 90
c = 160.234	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Fu, K., Rao, Y.J.

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Funding Organization	Location	Grant Number
Other private	China	2021YFC2102700
Other private	China	BK20202002
Other private	China	KYCX20_1812
Other government	China	KYCX20_1816

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release