7ZIW | pdb_00007ziw

X-ray structure of the haloalkane dehalogenase HaloTag7 bound to a butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (TMR-T4)

PDB DOI: https://doi.org/10.2210/pdb7ZIW/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: 1.99 Å
R-Value Free:
0.274 (Depositor), 0.274 (DCC)
R-Value Work:
0.248 (Depositor), 0.247 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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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 butyltrifluoromethanesulfonamide tetramethylrhodamine ligand (FSAm(4)-TMR)

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

To be published.

Macromolecule Content

Total Structure Weight: 67.9 kDa
Atom Count: 4,996
Modeled Residue Count: 586
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A3G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IYE (Subject of Investigation/LOI) Query on IYE Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	[9-[2-carboxy-5-[2-[2-[4-(trifluoromethylsulfonylamino)butoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C₃₄ H₄₀ F₃ N₄ O₈ S CKSQAQHVRBNIHM-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: 1.99 Å
R-Value Free: 0.274 (Depositor), 0.274 (DCC)
R-Value Work: 0.248 (Depositor), 0.247 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.171	α = 71.51
b = 49.795	β = 89.953
c = 78.718	γ = 67.994

Software Package:

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

Structure Validation

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.