9IM9 | pdb_00009im9

CTB10-M4-(S)-1d complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.201 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 34.13 kDa 
  • Atom Count: 2,296 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 282 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CTB10
A, B
141Cercospora sp. JNU001Mutation(s): 5 
UniProt
Find proteins for A0A977K7H6 (Cercospora sp. JNU001)
Explore A0A977K7H6 
Go to UniProtKB:  A0A977K7H6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A977K7H6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D9Q
(Subject of Investigation/LOI)

Query on A1D9Q



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
(3~{S})-1',1'-bis(chloranyl)-5-methyl-spiro[1~{H}-indole-3,2'-cyclopropane]-2-one
C11 H9 Cl2 N O
ZLVLBGNQLFDEAB-JTQLQIEISA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A],
H [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PBF
Query on PBF
A, B
L-PEPTIDE LINKINGC16 H15 N O3PHE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.201 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.384α = 90
b = 121.402β = 90
c = 160.533γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina2021YFC2102700
Other privateChinaBK20202002
Other privateChinaKYCX20_1812
Other privateChinaKYCX20_1816

Revision History  (Full details and data files)

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