2YJ7

Crystal structure of a hyperstable protein from the Precambrian period

• PDB DOI: https://doi.org/10.2210/pdb2YJ7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-19 Released: 2012-05-30 
• Deposition Author(s): Gavira, J.A., Ingles, A., Ibarra, B., Garcia-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Conservation of Protein Structure Over Four Billion Years

Ingles-Prieto, A., Ibarra-Molero, B., Delgado-Delgado, A., Perez-Jimenez, R., Fernandez, J.M., Gaucher, E.A., Sanchez-Ruiz, J.M., Gavira, J.A.

(2013) Structure 21: 1690

• PubMed: 23932589 
• DOI: https://doi.org/10.1016/j.str.2013.06.020
• Primary Citation of Related Structures:  
  2YJ7, 2YN1, 2YNX, 2YOI, 2YPM, 3ZIV, 4BA7


• PubMed Abstract: 
  

  Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis.

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Organizational Affiliation: 

Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada 18071, Spain.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.03 kDa 
• Atom Count: 2,104 
• Modelled Residue Count: 210 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPBCA THIOREDOXIN	A, B	106	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.072	α = 90
b = 30.189	β = 116.81
c = 59.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Gavira, J.A., Ingles, A., Ibarra, B., Garcia-Ruiz, J.M.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references, Other
• Version 1.2: 2013-09-25
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary