2XQZ | pdb_00002xqz

Neutron structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase

• PDB DOI: https://doi.org/10.2210/pdb2XQZ/pdb

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


• Deposited: 2010-09-08 Released: 2010-12-22 
• Deposition Author(s): Tomanicek, S.J., Wang, K.K., Weiss, K.L., Blakeley, M.P., Cooper, J., Chen, Y., Coates, L.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

The Active Site Protonation States of Perdeuterated Toho-1 Beta-Lactamase Determined by Neutron Diffraction Support a Role for Glu166 as the General Base in Acylation.

Tomanicek, S.J., Wang, K.K., Weiss, K.L., Blakeley, M.P., Cooper, J., Chen, Y., Coates, L.

(2011) FEBS Lett 585: 364

• PubMed: 21168411 
• DOI: https://doi.org/10.1016/j.febslet.2010.12.017
• Primary Citation Related Structures: 
  2XQZ, 2XR0


• PubMed Abstract: 
  

  Room temperature neutron diffraction data of the fully perdeuterated Toho-1 R274N/R276N double mutant β-lactamase in the apo form were used to visualize deuterium atoms within the active site of the enzyme. This perdeuterated neutron structure of the Toho-1 R274N/R276N reveals the clearest picture yet of the ground-state active site protonation states and the complete hydrogen-bonding network in a β-lactamase enzyme. The ground-state active site protonation states detailed in this neutron diffraction study are consistent with previous high-resolution X-ray studies that support the role of Glu166 as the general base during the acylation reaction in the class A β-lactamase reaction pathway.

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Organizational Affiliation: 
• Oak Ridge National Laboratory, Neutron Scattering Science Division, Oak Ridge, TN 37831, USA.

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: 27.99 kDa 
• Atom Count: 2,169 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMSE TOHO-1	A	260	Escherichia coli	Mutation(s): 2  EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.956	α = 90
b = 72.956	β = 90
c = 98.526	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
LAUEGEN	data reduction
LAUEGEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Tomanicek, S.J., Wang, K.K., Weiss, K.L., Blakeley, M.P., Cooper, J., Chen, Y., Coates, L.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 2.0: 2017-12-27
  Changes: Advisory, Atomic model, Derived calculations, Other
• Version 2.1: 2018-01-31
  Changes: Data collection
• Version 2.2: 2024-05-08
  Changes: Data collection, Database references