5FLW | pdb_00005flw

Crystal structure of putative exo-beta-1,3-galactanase from Bifidobacterium bifidum s17

• PDB DOI: https://doi.org/10.2210/pdb5FLW/pdb

• Classification: HYDROLASE
• Organism(s): Bifidobacterium bifidum S17
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-28 Released: 2015-12-23 
• Deposition Author(s): Godoy, A.S., de Lima, M.Z.T., Ramia, M.P., Camilo, C.M., Muniz, J.R.C., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17.

Godoy, A.S., de Lima, M.Z., Camilo, C.M., Polikarpov, I.

(2016) Acta Crystallogr F Struct Biol Commun 72: 288-293

• PubMed: 27050262 
• DOI: https://doi.org/10.1107/S2053230X16003617
• Primary Citation Related Structures: 
  5FLW


• PubMed Abstract: 
  

  Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues.

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Organizational Affiliation: 
• Departamento de Física em São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13560-970 São Carlos-SP, Brazil.
Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970 Piracicaba-SP, Brazil.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 68.3 kDa 
• Atom Count: 6,144 
• Modeled Residue Count: 604 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-BETA-1,3-GALACTANASE	A, B	304	Bifidobacterium bifidum S17	Mutation(s): 0  EC: 3.2.1.145

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	C [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.926	α = 90
b = 67.343	β = 90
c = 202.126	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Godoy, A.S., de Lima, M.Z.T., Ramia, M.P., Camilo, C.M., Muniz, J.R.C., Polikarpov, I.

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2016-03-30
  Changes: Database references, Structure summary
• Version 1.2: 2016-04-13
  Changes: Database references
• Version 1.3: 2016-04-20
  Changes: Database references
• Version 1.4: 2017-05-10
  Changes: Database references
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description