5Y2Y | pdb_00005y2y

Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-HaloTag ligand

• PDB DOI: https://doi.org/10.2210/pdb5Y2Y/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-07-27 Released: 2017-09-06 
• Deposition Author(s): Lee, H., Kang, M., Rhee, H., Lee, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure-guided synthesis of a protein-based fluorescent sensor for alkyl halides

Kang, M.G., Lee, H., Kim, B.H., Dunbayev, Y., Seo, J.K., Lee, C., Rhee, H.W.

(2017) Chem Commun (Camb) 53: 9226-9229

• PubMed: 28766590 
• DOI: https://doi.org/10.1039/c7cc03714g
• Primary Citation Related Structures: 
  5Y2X, 5Y2Y


• PubMed Abstract: 
  

  Alkyl halides are potentially mutagenic carcinogens. However, no efficient fluorescent sensor for alkyl halide detection in human-derived samples has been developed to date. Herein, we report a new protein-based fluorescent sensor for alkyl halides. Analysis of the HaloTag holo-crystal structure with its covalently attached ligand revealed an unexpected cavity, allowing for the design of a new fluorogenic ligand. This ligand showed the highest fluorescence response (300-fold) and fastest binding kinetics (t _1/2 < 150 s) to a HaloTag mutant (M175P) protein. This protein-based sensor system was effectively used to detect alkyl halides in human serum and monitor real-time protein alkylation.

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Organizational Affiliation: 
• Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.35 kDa 
• Atom Count: 5,048 
• Modeled Residue Count: 583 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A, B	299	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 22  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8LL (Subject of Investigation/LOI)	C [auth A], E [auth B]	5-(dimethylamino)-~{N}-[2-(2-hexoxyethoxy)ethyl]naphthalene-1-sulfonamide C22 H34 N2 O4 S ZQDZHRAPTBKCCR-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.393	α = 90
b = 72.355	β = 90
c = 174.942	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
PHENIX	phasing
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Lee, H., Kang, M., Rhee, H., Lee, C.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary