7PCX

X-RAY STRUCTURE OF THE HALOALKANE DEHALOGENASE HALOTAG7-Q165W LABELED WITH A CHLOROALKANE-TETRAMETHYLRHODAMINE FLUOROPHORE SUBSTRATE

PDB DOI: https://doi.org/10.2210/pdb7PCX/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: 1.40 Å
R-Value Free: 0.198
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.2 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41592-021-01341-x
Primary Citation of 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: 204.38 kDa
Atom Count: 15,752
Modelled Residue Count: 1,758
Deposited Residue Count: 1,758
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A, B, C, D, E A, B, C, D, E, F	293	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A3G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain W [auth F]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], W [auth F]	[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 G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain W [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], V [auth E], Y [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain X [auth F]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], X [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain X [auth F]