5FLW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1107/S2053230X16003617

  • 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 ...

    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.


    Organizational Affiliation

    Departamento de Física em São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13560-970 São Carlos-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXO-BETA-1,3-GALACTANASE
A, B
304Bifidobacterium bifidum (strain S17)N/A
Find proteins for E3END6 (Bifidobacterium bifidum (strain S17))
Go to UniProtKB:  E3END6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download SDF File 
Download CCD File 
B
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.926α = 90.00
b = 67.343β = 90.00
c = 202.126γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references, Structure summary
  • Version 1.2: 2016-04-13
    Type: Database references
  • Version 1.3: 2016-04-20
    Type: Database references
  • Version 1.4: 2017-05-10
    Type: Database references