6SS3 | pdb_00006ss3

Kemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole

• PDB DOI: https://doi.org/10.2210/pdb6SS3/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-09-06 Released: 2020-04-01 
• Deposition Author(s): Bloch, J.S., Pinkas, D.M., Hilvert, D.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency

Kries, H., Bloch, J.S., Bunzel, H.A., Pinkas, D.M., Hilvert, D.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c00575

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.53 kDa 
• Atom Count: 6,092 
• Modeled Residue Count: 604 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase HG3.17 Q50K, E47N, N300D	A, B	318	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NT	C [auth A], F [auth B]	6-NITROBENZOTRIAZOLE C6 H4 N4 O2 AOCDQWRMYHJTMY-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.08	α = 90
b = 78.28	β = 90
c = 98.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Bloch, J.S., Pinkas, D.M., Hilvert, D.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary