Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 29.33 kDa 
• Atom Count: 2264 
• Residue Count: 251 
• Unique protein chains: 1

6C7T

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 20 round 5

• DOI: 10.2210/pdb6C7T/pdb

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


• Deposited: 2018-01-23 Released: 2018-08-01 
• Deposition Author(s): Jackson, C.J., Hong, N.-S., Carr, P.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.216 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

The evolution of multiple active site configurations in a designed enzyme.

Hong, N.S., Petrovic, D., Lee, R., Gryn'ova, G., Purg, M., Saunders, J., Bauer, P., Carr, P.D., Lin, C.Y., Mabbitt, P.D., Zhang, W., Altamore, T., Easton, C., Coote, M.L., Kamerlin, S.C.L., Jackson, C.J.

(2018) Nat Commun 9: 3900-3900

• PubMed: 30254369 
• DOI: 10.1038/s41467-018-06305-y
• Primary Citation of Related Structures:  
  6CT3, 6DC1, 6DKV, 6DNJ, 6C7H, 6C8B, 6C7T, 6C7V, 6C7M, 6CAI


• PubMed Abstract: 
  

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.

---

Organizational Affiliation: 

Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase KE07	A	264	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.216 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.765	α = 90
b = 97.765	β = 90
c = 157.027	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-23 
• Released Date: 2018-08-01 
Deposition Author(s): Jackson, C.J., Hong, N.-S., Carr, P.D.

Revision History 

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2019-02-13
  Changes: Data collection, Database references