8B6Q | pdb_00008b6q

X-ray structure of the haloalkane dehalogenase HaloTag7 with an insertion of Calmodulin-M13 fusion at position 154-156 that mimic the structure of CaProLa, an calcium gated protein labeling technology

PDB DOI: https://doi.org/10.2210/pdb8B6Q/pdb

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

Deposited: 2022-09-27 Released: 2023-10-11
Deposition Author(s): Tarnawski, M., Johnsson, K., Hiblot, J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.318 (Depositor), 0.317 (DCC)
R-Value Work:
0.281 (Depositor), 0.281 (DCC)
R-Value Observed:
0.282 (Depositor)

Starting Models: experimental
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This is version 1.1 of the entry. See complete history.

Literature

X-ray structure of the haloalkane dehalogenase HaloTag7 with an insertion of Calmodulin-M13 fusion at position 154-156 that mimic the structure of CaProLa, an calcium gated protein labeling technology

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

To be published.

Macromolecule Content

Total Structure Weight: 53.22 kDa
Atom Count: 3,699
Modeled Residue Count: 466
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase,Calmodulin-1,Haloalkane dehalogenase,Calmodulin-1,M13 peptide	A	472	Rhodococcus sp. (in: high G+C Gram-positive bacteria), Homo sapiens	Mutation(s): 20 Gene Names: dhaA, CALM1, CALM, CAM, CAM1 EC: 3.8.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3 Go to UniProtKB: P0A3G3
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23 Go to UniProtKB: P0DP23
PHAROS: P0DP23 GTEx: ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0DP23 P0A3G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.318 (Depositor), 0.317 (DCC)
R-Value Work: 0.281 (Depositor), 0.281 (DCC)
R-Value Observed: 0.282 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.53	α = 90
b = 74.53	β = 90
c = 177.84	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2023-10-11
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.