5Y2X

Crystal structure of apo-HaloTag (M175C)

• PDB DOI: https://doi.org/10.2210/pdb5Y2X/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: 2.02 Å
• R-Value Free: 0.192 
• R-Value Work: 0.163 

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 of 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

Macromolecule Content

• Total Structure Weight: 33.75 kDa 
• Atom Count: 2,625 
• Modelled Residue Count: 295 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.192 
• R-Value Work: 0.163 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.642	α = 90
b = 62.642	β = 90
c = 164.192	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: Data collection, Database references, Refinement description