3HH4 | pdb_00003hh4

New azaborine compounds bind to the T4 lysozyme L99A cavity - Benzene as control

• PDB DOI: https://doi.org/10.2210/pdb3HH4/pdb

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


• Deposited: 2009-05-14 Released: 2009-10-13 
• Deposition Author(s): Liu, L., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Boron mimetics: 1,2-dihydro-1,2-azaborines bind inside a nonpolar cavity of T4 lysozyme.

Liu, L., Marwitz, A.J., Matthews, B.W., Liu, S.Y.

(2009) Angew Chem Int Ed Engl 48: 6817-6819

• PubMed: 19688806 
• DOI: https://doi.org/10.1002/anie.200903390
• Primary Citation of Related Structures:  
  3HH3, 3HH4, 3HH5, 3HH6

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Organizational Affiliation: 
• Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1253, 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: 19.07 kDa 
• Atom Count: 1,718 
• Modeled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	164	Tequatrovirus T4	Mutation(s): 3  Gene Names: E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HED	B [auth A], C [auth A]	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BNZ	E [auth A]	BENZENE C6 H6 UHOVQNZJYSORNB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60	α = 90
b = 60	β = 90
c = 95.65	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Liu, L., Matthews, B.W.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description