Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 69.79 kDa 
• Atom Count: 5200 
• Modelled Residue Count: 598 
• Deposited Residue Count: 624 
• Unique protein chains: 1

3A2M

CRYSTAL STRUCTURE OF DBJA (WILD TYPE Type I)

• PDB DOI: 10.2210/pdb3A2M/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-23 Released: 2010-05-26 
• Deposition Author(s): Sato, Y., Senda, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.187 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

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: 10.1002/anie.201001753
• Primary Citation of Related Structures:  
  3A2L, 3A2M, 3A2N, 3AFI

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A, B	312	Bradyrhizobium japonicum	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D, E	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D, E	sucrose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.187 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.577	α = 90
b = 48.866	β = 97.36
c = 106.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-23 
• Released Date: 2010-05-26 
Deposition Author(s): Sato, Y., Senda, T.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary