8J1O | pdb_00008j1o

Crystal structure of HaloTag complexed with BTTA

• PDB DOI: https://doi.org/10.2210/pdb8J1O/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-04-13 Released: 2024-04-17 
• Deposition Author(s): Kim, H., Rhee, H., Lee, C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

GEN-Click: Genetically Encodable Click Reactions for Spatially Restricted Metabolite Labeling.

Mishra, P.K., Sharma, N., Kim, H., Lee, C., Rhee, H.W.

(2023) ACS Cent Sci 9: 1650-1657

• PubMed: 37637744 
• DOI: https://doi.org/10.1021/acscentsci.3c00511
• Primary Citation of Related Structures:  
  8J1O


• PubMed Abstract: 
  

  Chemical reactions for the in situ modification of biomolecules within living cells are under development. Among these reactions, bio-orthogonal reactions such as click chemistry using copper(I) and Staudinger ligation are widely used for specific biomolecule tracking in live systems. However, currently available live cell copper(I)-catalyzed azide/alkyne cycloaddition reactions are not designed in a spatially resolved manner. Therefore, we developed the "GEN-Click" system, which can target the copper(I)-catalyzed azide/alkyne cycloaddition reaction catalysts proximal to the protein of interest and can be genetically expressed in a live cell. The genetically controlled, spatially restricted, metal-catalyzed biorthogonal reaction can be used for proximity biotin labeling of various azido-bearing biomolecules (e.g., protein, phospholipid, oligosaccharides) in living cell systems. Using GEN-Click, we successfully detected local metabolite-transferring events at cell-cell contact sites.

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Organizational Affiliation: 
• Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.

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: 33.89 kDa 
• Atom Count: 2,676 
• Modeled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	294	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TN9 (Subject of Investigation/LOI)	B [auth A]	N-[[1-[2-[2-(2-hexoxyethoxy)ethoxy]ethyl]-1,2,3-triazol-4-yl]methyl]-1-(1H-1,2,3-triazol-4-yl)-N-(2H-1,2,3-triazol-4-ylmethyl)methanamine C21 H36 N10 O3 TULQAAWRGBJEDU-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.088	α = 90
b = 63.088	β = 90
c = 163.681	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Kim, H., Rhee, H., Lee, C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021M3A9G8022417

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2025-10-29
  Changes: Database references, Structure summary