10YL | pdb_000010yl

Crystal structure of a computationally designed protein, dnMSBP, apo form

• PDB DOI: https://doi.org/10.2210/pdb10YL/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-02-12 Released: 2026-09-30 
• Deposition Author(s): Wang, J.-X., Lu, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: in silico

Literature

De Novo Design and Structural Optimization of Mn(salen)-Based Artificial Metalloenzymes for Asymmetric Sulfoxidation.

Wang, J.X., Deng, Y., Kalvet, I., Haque, A., Dai, H., Baker, D., Lu, Y.

(2026) Angew Chem Int Ed Engl : e5852828-e5852828

• PubMed: 42758048 
• DOI: https://doi.org/10.1002/anie.5852828
• Primary Citation Related Structures: 
  10YL, 10YM, 10YP, 10YR


• PubMed Abstract: 
  

  Artificial metalloenzymes (ArMs) exhibit exceptional selectivity, yet extending their reactivity beyond native cofactors remains a major challenge. While previous designs using native protein scaffolds to incorporate nonnative cofactors have been reported, de novo protein design enables tailored scaffolds that incorporate nonnative cofactors, unlocking transformations inaccessible to natural enzymes. Here, we report the computational design of de novo proteins that bind Mn(salen)-based complexes for asymmetric sulfoxidation. The resulting ArMs outperform the free cofactor, achieving up to 45% yield and an enantiomeric ratio (e.r.) of 26:74 under optimized conditions. A 1.5 Å resolution crystal structure confirms the designed architecture and reveals key secondary-sphere interactions that govern reactivity. Guided by these insights, rational mutagenesis enhanced performance up to 79% yield and an e.r. up to 16:84. This work establishes a general strategy for integrating complex nonnative cofactors into de novo scaffolds, enabling selective catalysts for reactions beyond the reach of natural enzymes.

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Organizational Affiliation: 
• Department of Chemistry, University of Texas at Austin, Austin, Texas, USA.
Department of Chemistry and Biochemistry, St. Mary's College of Maryland, St. Mary's City, Maryland, USA.
Department of Biochemistry, University of Washington, Seattle, Washington, USA.
Institute For Protein Design, University of Washington, Seattle, Washington, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.85 kDa 
• Atom Count: 1,620 
• Modeled Residue Count: 211 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dnMSBP	A	232	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.262 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.484	α = 90
b = 119.484	β = 90
c = 119.484	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
xia2	data scaling
xia2	data reduction
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Wang, J.-X., Lu, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release