5JWT

T4 Lysozyme L99A/M102Q with Benzene Bound

• PDB DOI: https://doi.org/10.2210/pdb5JWT/pdb

• Classification: HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-05-12 Released: 2016-09-21 
• Deposition Author(s): Lee, H., Fischer, M., Shoichet, B.K., Liu, S.-Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.243 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.

Lee, H., Fischer, M., Shoichet, B.K., Liu, S.Y.

(2016) J Am Chem Soc 138: 12021-12024

• PubMed: 27603116 
• DOI: https://doi.org/10.1021/jacs.6b06566
• Primary Citation of Related Structures:  
  5JWS, 5JWT, 5JWU, 5JWV, 5JWW


• PubMed Abstract: 
  

  Protein crystallography and calorimetry were used to characterize the binding of 1,2-azaborines to model cavities in T4 lysozyme in direct comparison to their carbonaceous counterparts. In the apolar L99A cavity, affinity for Ab dropped only slightly versus benzene. In the cavity designed to accommodate a single hydrogen bond (L99A/M102Q), Gln102═O···H-N hydrogen bonding for Ab and BEtAb was observed in the crystallographic complexes. The strength of the hydrogen bonding was estimated as 0.94 and 0.64 kcal/mol for Ab and BEtAb, respectively. This work unambiguously demonstrates that 1,2-azaborines can be readily accommodated in classic aryl recognition pockets and establishes one of 1,2-azaborine's distinguishing features from its carbonaceous isostere benzene: its ability to serve as an NH hydrogen bond donor in a biological setting.

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Organizational Affiliation: 

Department of Chemistry, Boston College , Chestnut Hill, Massachusetts 02467, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.72 kDa 
• Atom Count: 1,676 
• Modelled Residue Count: 161 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin	A	164	Tequatrovirus T4	Mutation(s): 6  EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNZ	B [auth A]	BENZENE C6 H6 UHOVQNZJYSORNB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.243 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.23	α = 90
b = 60.23	β = 90
c = 96.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
PHENIX	model building
PHENIX	phasing
d*TREK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Lee, H., Fischer, M., Shoichet, B.K., Liu, S.-Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5001989

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2022-04-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Refinement description