5D2T

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 3 Wild Type

• PDB DOI: https://doi.org/10.2210/pdb5D2T/pdb

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


• Deposited: 2015-08-06 Released: 2016-09-07 
• Deposition Author(s): Jackson, C.J., Hong, N.-S., Carr, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.232 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 1 Wild Type

Hong, N.-S., Jackson, C.J., Carr, P.D.

To be published.

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: 29.32 kDa 
• Atom Count: 2,224 
• Modelled Residue Count: 251 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed kemp eliminase KE07	A	264	synthetic construct	Mutation(s): 0  EC: 4.1.3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6VP	B [auth A]	5-nitro-2-oxidanyl-benzenecarbonitrile C7 H4 N2 O3 MPQNPFJBRPRBFF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.232 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.338	α = 90
b = 96.338	β = 90
c = 155.323	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Jackson, C.J., Hong, N.-S., Carr, P.D.

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description