7ZIV | pdb_00007ziv

X-ray structure of the haloalkane dehalogenase dead variant HaloTag7-D106A bound to a chloroalkane tetramethylrhodamine fluorophore ligand (CA-TMR)

• PDB DOI: https://doi.org/10.2210/pdb7ZIV/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the haloalkane dehalogenase dead variant HaloTag7-D106A bound to a chloroalkane tetramethylrhodamine fluorophore ligand (CA-TMR)

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.95 kDa 
• Atom Count: 2,650 
• Modeled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OEH (Subject of Investigation/LOI)	B [auth A]	[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
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.01	α = 90
b = 77.35	β = 118.525
c = 44.29	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-19 
Deposition Author(s): Tarnawski, M., Kompa, J., Johnsson, K., Hiblot, J.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

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