Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17357.99 
• Atom Count: 1143 
• Residue Count: 151 
• Unique protein chains: 1

4S0L

Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79V, and F123V mutant

• DOI: 10.2210/pdb4S0L/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus abyssi (strain GE5 / Orsay)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 6 


• Deposited: 2014-12-31 Released: 2015-03-18 
• Deposition Author(s): Pearson, A.D., Mills, J.H., Song, Y., Nasertorabi, F., Han, G.W., Baker, D., Stevens, R.C., Schultz, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.223 
• R-Value Work: 0.177 

Literature

Transition states. Trapping a transition state in a computationally designed protein bottle.

Pearson, A.D., Mills, J.H., Song, Y., Nasertorabi, F., Han, G.W., Baker, D., Stevens, R.C., Schultz, P.G.

(2015) Science 347: 863-867

• PubMed: 25700516 
• DOI: 10.1126/science.aaa2424
• Primary Citation of Related Structures:  
  4S0K, 4S0J, 4S0I, 4S03, 4S02


• PubMed Abstract: 
  

The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.

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Organizational Affiliation: 

Department of Chemistry, and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Threonine--tRNA ligase	A	151	Pyrococcus abyssi (strain GE5 / Orsay)	Mutation(s): 6  Gene Names: thrS EC: 6.1.1.3
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay)) Go to UniProtKB:  Q9UZ14

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BIF	A	L-PEPTIDE LINKING	C15 H15 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.223 
• R-Value Work: 0.177 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 52.096	α = 90.00
b = 78.746	β = 90.00
c = 91.407	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data scaling
REFMAC	refinement
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-31 
• Released Date: 2015-03-18 
• Deposition Author(s): Pearson, A.D., Mills, J.H., Song, Y., Nasertorabi, F., Han, G.W., Baker, D., Stevens, R.C., Schultz, P.G.

Revision History 

• Version 1.0: 2015-03-18
  Type: Initial release
• Version 1.1: 2017-11-22
  Type: Refinement description