7ZIX

X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (TMR-S4)

PDB DOI: https://doi.org/10.2210/pdb7ZIX/pdb

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

Deposited: 2022-04-08 Released: 2023-04-19
Deposition Author(s): Tarnawski, M., Kompa, J., Johnsson, K., Hiblot, J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.222
R-Value Work: 0.197
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butylmethanesulfonamide tetramethylrhodamine ligand (HSAm(4)-TMR)

Tarnawski, M., Kompa, J., Johnsson, K., Hiblot, J.

To be published.

Macromolecule Content

Total Structure Weight: 67.79 kDa
Atom Count: 4,939
Modelled Residue Count: 586
Deposited Residue Count: 586
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A3G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IYU (Subject of Investigation/LOI) Query on IYU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	[9-[2-carboxy-5-[2-[2-[4-(methylsulfonylamino)butoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C₃₄ H₄₃ N₄ O₈ S DSUCSFUEKBFNJW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.222
R-Value Work: 0.197
R-Value Observed: 0.198
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.227	α = 90
b = 78.399	β = 92.571
c = 81.623	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
STARANISO	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.