5E9A

Crystal structure analysis of the cold-adamped beta-galactosidase from Rahnella sp. R3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.561 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cloning, expression and structural stability of a cold-adapted beta-galactosidase from Rahnella sp. R3.

Fan, Y.Hua, X.Zhang, Y.Feng, Y.Shen, Q.Dong, J.Zhao, W.Zhang, W.Jin, Z.Yang, R.

(2015) Protein Expr.Purif. 115: 158-164

  • DOI: 10.1016/j.pep.2015.07.001

  • PubMed Abstract: 
  • A novel gene was isolated for the first time from a psychrophilic gram-negative bacterium Rahnella sp. R3. The gene encoded a cold-adapted β-galactosidase (R-β-Gal). Recombinant R-β-Gal was expressed in Escherichia coli BL21 (DE3), purified and chara ...

    A novel gene was isolated for the first time from a psychrophilic gram-negative bacterium Rahnella sp. R3. The gene encoded a cold-adapted β-galactosidase (R-β-Gal). Recombinant R-β-Gal was expressed in Escherichia coli BL21 (DE3), purified and characterized. R-β-gal belongs to the glycosyl hydrolase family 42. Circular dichroism spectrometry of the structural stability of R-β-Gal with respect to temperature indicated that the secondary structures of the enzyme were stable to 45°C. In solution, the enzyme was a homo-trimer and was active at temperatures as low as 4°C. The enzyme did not require the presence of metal ions to be active, but Mg(2+), Mn(2+), and Ca(2+) enhanced its activity slightly, whereas Fe(3+), Zn(2+) and Al(3+) appeared to inactive it. The purified enzyme displayed K(m) values of 6.5 mM for ONPG and 2.2mM for lactose at 4°C. These values were lower than the corresponding K(m)s reported for other cold-adapted β-Gals.


    Organizational Affiliation

    State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China. Electronic address: yilin58299@163.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D, E, F
712Rahnella sp. R3Mutation(s): 0 
EC: 3.2.1.23
Find proteins for A0A0B4U8I5 (Rahnella sp. R3)
Go to UniProtKB:  A0A0B4U8I5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.561 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 146.426α = 90.00
b = 106.831β = 109.00
c = 164.244γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-14 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Zhang, Y.Z., Fan, Y.T.

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references, Derived calculations, Structure summary