7O8B

Structure of haloalkane dehalogenase variant DhaA80 from Rhodococcus rhodochrous

• PDB DOI: https://doi.org/10.2210/pdb7O8B/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus rhodochrous
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-04-15 Released: 2021-09-08 
• Deposition Author(s): Shaposhnikova, A., Prudnikova, T., Kuta Smatanova, I.
• Funding Organization(s): Grant Agency of the Czech Republic, German Federal Ministry for Education and Research, European Regional Development Fund, Ministry of Education (MoE, Czech Republic)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.224 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids

Shaposhnikova, A., Kuty, M., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I., Minofar, B., Prudnikova, T.

(2021) Crystals (Basel) 11

• DOI: https://doi.org/10.3390/cryst11091052

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.2 kDa 
• Atom Count: 2,502 
• Modelled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	290	Rhodococcus rhodochrous	Mutation(s): 4  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G2 (Rhodococcus rhodochrous) Explore P0A3G2  Go to UniProtKB:  P0A3G2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V5B (Subject of Investigation/LOI)	B [auth A]	methyl sulfate C H4 O4 S JZMJDSHXVKJFKW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.224 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.889	α = 90
b = 69.551	β = 90
c = 83.916	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Shaposhnikova, A., Prudnikova, T., Kuta Smatanova, I.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	17-24321S
German Federal Ministry for Education and Research	Germany	DAAD-16-09
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000441
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_019/0000778
European Regional Development Fund	Czech Republic	LM2015047
European Regional Development Fund	Czech Republic	LM2018121
Ministry of Education (MoE, Czech Republic)	Czech Republic	CZ.02.1.01/0.0/0.0/16_026/0008451

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description