7PCW | pdb_00007pcw

X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-M175W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE

PDB DOI: https://doi.org/10.2210/pdb7PCW/pdb

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

Deposited: 2021-08-04 Released: 2021-12-15
Deposition Author(s): Tarnawski, M., Frei, M., Hiblot, J., Johnsson, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Engineered HaloTag variants for fluorescence lifetime multiplexing.

Frei, M.S., Tarnawski, M., Roberti, M.J., Koch, B., Hiblot, J., Johnsson, K.

(2022) Nat Methods 19: 65-70

PubMed: 34916672 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41592-021-01341-x
Primary Citation Related Structures:
6ZVY, 7PCW, 7PCX

PubMed Abstract:
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.

Organizational Affiliation

Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 135.81 kDa
Atom Count: 9,711
Modeled Residue Count: 1,170
Deposited Residue Count: 1,172
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A, B, C, D	293	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 21 Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3 Go to UniProtKB: P0A3G3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A3G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OEH (Subject of Investigation/LOI) Query on OEH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	[9-[2-carboxy-5-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C₃₅ H₄₃ Cl N₃ O₆ YORHEDWUCXZZLS-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]