3AFI

Crystal structure of DBJA (HIS-DBJA)

• PDB DOI: https://doi.org/10.2210/pdb3AFI/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium diazoefficiens USDA 110
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-02 Released: 2011-01-19 
• Deposition Author(s): Sato, Y., Senda, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.191 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering

Prokop, Z., Sato, Y., Brezovsky, J., Mozga, T., Chaloupkova, R., Koudelakova, T., Jerabek, P., Stepankova, V., Natsume, R., van Leeuwen, J.G., Janssen, D.B., Florian, J., Nagata, Y., Senda, T., Damborsky, J.

(2010) Angew Chem Int Ed Engl 49: 6111-6115

• PubMed: 20645368 
• DOI: https://doi.org/10.1002/anie.201001753
• Primary Citation of Related Structures:  
  3A2L, 3A2M, 3A2N, 3AFI

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Organizational Affiliation: 

Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.98 kDa 
• Atom Count: 10,545 
• Modelled Residue Count: 1,204 
• Deposited Residue Count: 1,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A [auth E], B [auth A], C [auth B], D [auth F]	316	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0  Gene Names: DBJA EC: 3.8.1.5
UniProt
Find proteins for P59337 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore P59337  Go to UniProtKB:  P59337

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E, F [auth A], G [auth B], H [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.191 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.855	α = 90
b = 117.843	β = 90
c = 55.796	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Sato, Y., Senda, T.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description