7Q3J | pdb_00007q3j

Computationally designed thioredoxin subjected to stability optimizing mutations.

• PDB DOI: https://doi.org/10.2210/pdb7Q3J/pdb

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


• Deposited: 2021-10-27 Released: 2022-11-16 
• Deposition Author(s): Norrild, R.K., Johansson, K.E., O'Shea, C., Lindorff-Larsen, K., Winther, J.R., Morth, J.P.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Increasing protein stability by inferring substitution effects from high-throughput experiments.

Norrild, R.K., Johansson, K.E., O'Shea, C., Morth, J.P., Lindorff-Larsen, K., Winther, J.R.

(2022) Cell Rep Methods 2: 100333-100333

• PubMed: 36452862 
• DOI: https://doi.org/10.1016/j.crmeth.2022.100333
• Primary Citation Related Structures: 
  7Q3J, 7Q3K


• PubMed Abstract: 
  

  We apply a computational model, global multi-mutant analysis (GMMA), to inform on effects of most amino acid substitutions from a randomly mutated gene library. Using a high mutation frequency, the method can determine mutations that increase the stability of even very stable proteins for which conventional selection systems have reached their limit. As a demonstration of this, we screened a mutant library of a highly stable and computationally redesigned model protein using an in vivo genetic sensor for folding and assigned a stability effect to 374 of 912 possible single amino acid substitutions. Combining the top 9 substitutions increased the unfolding energy 47 to 69 kJ/mol in a single engineering step. Crystal structures of stabilized variants showed small perturbations in helices 1 and 2, which rendered them closer in structure to the redesign template. This case study illustrates the capability of the method, which is applicable to any screen for protein function.

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Organizational Affiliation: 
• Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.94 kDa 
• Atom Count: 1,532 
• Modeled Residue Count: 176 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MM9	A, B	114	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.89	α = 90
b = 45.656	β = 92.155
c = 72.882	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Norrild, R.K., Johansson, K.E., O'Shea, C., Lindorff-Larsen, K., Winther, J.R., Morth, J.P.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2023-03-01
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description