8RD5

Crystal structure of Kemp Eliminase HG3.R5 with bound transition state analog 6-nitrobenzotriazole

• PDB DOI: https://doi.org/10.2210/pdb8RD5/pdb

• Classification: HYDROLASE
• Organism(s): Thermoascus aurantiacus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-12-07 Released: 2024-09-04 
• Deposition Author(s): Schaub, D., Schwander, T., Hueppi, S., Buller, R.M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.142 
• R-Value Work: 0.103 

Starting Model: experimental

Literature

Enriching productive mutational paths accelerates enzyme evolution

Patsch, D., Voss, M., Schwander, T., Schaub, D., Hueppi, S., Eichenberger, M., Bornscheuer, U.T., Hilvert, D., Buller, R.M.

To be published.

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: 69.66 kDa 
• Atom Count: 5,331 
• Modelled Residue Count: 600 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A, B	318	Thermoascus aurantiacus	Mutation(s): 27  Gene Names: XYNA
UniProt
Find proteins for P23360 (Thermoascus aurantiacus) Explore P23360  Go to UniProtKB:  P23360

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NT (Subject of Investigation/LOI)	C [auth A], H [auth B]	6-NITROBENZOTRIAZOLE C6 H4 N4 O2 AOCDQWRMYHJTMY-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.142 
• R-Value Work: 0.103 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.414	α = 100.723
b = 50.069	β = 102.703
c = 65.584	γ = 99.299

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Schaub, D., Schwander, T., Hueppi, S., Buller, R.M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	180544

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-09-18
  Changes: Database references