3A2L

Crystal structure of DBJA (mutant dbja delta)

• PDB DOI: https://doi.org/10.2210/pdb3A2L/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: 1.78 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

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)

Macromolecule Content

• Total Structure Weight: 69.17 kDa 
• Atom Count: 4,976 
• Modelled Residue Count: 584 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A, B	309	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	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [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	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.547	α = 90
b = 48.652	β = 97.39
c = 106.816	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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 1.2: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary