6S42

The double mutant(Ile44Leu+Gln102His) of haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 with an eliminated halide-binding site

• PDB DOI: https://doi.org/10.2210/pdb6S42/pdb

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


• Deposited: 2019-06-26 Released: 2020-02-05 
• Deposition Author(s): Pudnikova, T., Mesters, J.R., Kuta Smatanova, I.
• Funding Organization(s): Grant Agency of the Czech Republic, German Federal Ministry for Education and Research, European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.152 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 

Literature

Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site

Prudnikova, T., Kuta Smatanova, I.

(2019) Crystals (Basel) 

• DOI: https://doi.org/10.3390/cryst9070375

Biological Assembly 1  

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,822 
• Modelled Residue Count: 292 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	310	Bradyrhizobium elkanii	Mutation(s): 2  Gene Names: dbeA, dhaA EC: 3.8.1.5
UniProt
Find proteins for E2RV62 (Bradyrhizobium elkanii) Explore E2RV62  Go to UniProtKB:  E2RV62

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
HEZ (Subject of Investigation/LOI)	B [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.152 
• R-Value Work: 0.140 
• R-Value Observed: 0.140 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.945	α = 90
b = 63.95	β = 106.27
c = 46.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Pudnikova, T., Mesters, J.R., 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-16-19
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000441
European Regional Development Fund	Czech Republic	LM2015055

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description