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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (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 dead variant HaloTag7-D106A bound to a chloroalkane tetramethylrhodamine fluorophore ligand (CA-TMR)

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

To be published.

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

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(by identity cutoff) | 3D Structure

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
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.195 (Depositor), 0.200 (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

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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 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.