Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 52.84 kDa 
• Atom Count: 3822 
• Modelled Residue Count: 443 
• Deposited Residue Count: 469 
• Unique protein chains: 1

4COT

The importance of the Abn2 calcium cluster in the endo-1,5- arabinanase activity from Bacillus subtilis

• DOI: 10.2210/pdb4COT/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-01-31 Released: 2014-03-05 
• Deposition Author(s): McVey, C.E., Ferreira, M.J., Correia, B., Lahiri, S., deSanctis, D., Carrondo, M.A., Lindley, P.F., de Sa-Nogueira, I., Soares, C.M., Bento, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

The Importance of the Abn2 Calcium Cluster in the Endo-1,5-Arabinanase Activity from Bacillus Subtilis.

Mcvey, C.E., Ferreira, M.J., Correia, B., Lahiri, S., De Sanctis, D., Carrondo, M.A., Lindley, P.F., De Sa Nogueira, I., Soares, C.M., Bento, I.

(2014) J Biol Inorg Chem 19: 505

• PubMed: 24549757 
• DOI: 10.1007/s00775-014-1105-x
• Primary Citation of Related Structures:  
  4COT


• PubMed Abstract: 
  

Arabinanase is a glycosyl hydrolase that is able to cleave the glycosidic bonds of α-1,5-L-arabinan, releasing arabino-oligosaccharides and L-arabinose. The enzyme has two domains, an N-terminal catalytic domain with a characteristic β-propeller fold and a C-terminal domain whose function is unknown. A calcium ion, located near the catalytic site, serves to stabilize the N-terminal domain, but it has also been proposed to play a key role in the enzyme mechanism. The present work describes the structure of an inactive mutant of the wild-type enzyme (H318Q) and in which the calcium ion has been adventitiously replaced by nickel. These structural studies, together with functional and modelling studies, clearly support the role of the calcium ion in the overall reaction mechanism.

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Organizational Affiliation: 

Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Protugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR ENDO-ALPHA-(1->5)-L-ARABINANASE 2	A	469	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1  Gene Names: abn2, J3A, yxiA, BSU39330 EC: 3.2.1.99
Find proteins for P42293 (Bacillus subtilis (strain 168)) Explore P42293  Go to UniProtKB:  P42293

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.19	α = 90
b = 76.552	β = 112.6
c = 58.073	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-31 
• Released Date: 2014-03-05 
Deposition Author(s): McVey, C.E., Ferreira, M.J., Correia, B., Lahiri, S., deSanctis, D., Carrondo, M.A., Lindley, P.F., de Sa-Nogueira, I., Soares, C.M., Bento, I.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-03-26
  Changes: Atomic model
• Version 1.2: 2014-06-04
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other