8AH9 | pdb_00008ah9

De novo retro-aldolase RAbetaB-16.1

• PDB DOI: https://doi.org/10.2210/pdb8AH9/pdb

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


• Deposited: 2022-07-21 Released: 2023-08-16 
• Deposition Author(s): Mittl, P., Oualb Chaib, A., Hilvert, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 

Literature

Design and optimization of enzymatic activity in a de novo beta-barrel scaffold.

Kipnis, Y., Chaib, A.O., Vorobieva, A.A., Cai, G., Reggiano, G., Basanta, B., Kumar, E., Mittl, P.R.E., Hilvert, D., Baker, D.

(2022) Protein Sci 31: e4405-e4405

• PubMed: 36305767 
• DOI: https://doi.org/10.1002/pro.4405
• Primary Citation of Related Structures:  
  8AH9


• PubMed Abstract: 
  

  While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded β-barrel protein to create catalysts for a retro-aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, USA.
Institute for Protein Design, University of Washington, Seattle, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, USA.
Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.
VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.
Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.25 kDa 
• Atom Count: 1,060 
• Modeled Residue Count: 115 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAbetaB-16.1	A	120	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	B [auth A], C [auth A], D [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.482	α = 90
b = 77.485	β = 90
c = 60.652	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Mittl, P., Oualb Chaib, A., Hilvert, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Structure summary