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

Experimental Data Snapshot

  • Resolution: 2.56 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.pep.2015.07.001
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
712Rahnella sp. R3Mutation(s): 0 
Find proteins for A0A0B4U8I5 (Rahnella sp. R3)
Explore A0A0B4U8I5 
Go to UniProtKB:  A0A0B4U8I5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B4U8I5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.56 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.426α = 90
b = 106.831β = 109
c = 164.244γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references