6EVS

Characterization of 2-deoxyribosyltransferase from psychrotolerant bacterium Bacillus psychrosaccharolyticus: a suitable biocatalyst for the industrial synthesis of antiviral and antitumoral nucleosides

• PDB DOI: https://doi.org/10.2210/pdb6EVS/pdb

• Classification: TRANSFERASE
• Organism(s): Peribacillus psychrosaccharolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-02 Released: 2018-11-14 
• Deposition Author(s): Fresco-Tabohada, A., Fernandez-Lucas, J., Acebal, C., Arroyo, M., Ramon, F., Mancheno, J.M., de la Mata, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

2'-Deoxyribosyltransferase from Bacillus psychrosaccharolyticus: A Mesophilic-Like Biocatalyst for the Synthesis of Modified Nucleosides from a Psychrotolerant Bacterium

Fresco-Tabohada, A., Fernandez-Lucas, J., Acebal, C., Arroyo, M., Ramon, F., de la Mata, I., Mancheno, J.M.

(2019) Catalysts 

• DOI: https://doi.org/10.3390/catal8010008

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 32.83 kDa 
• Atom Count: 2,361 
• Modelled Residue Count: 274 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-deoxyribosyltransferase	A, B	142	Peribacillus psychrosaccharolyticus	Mutation(s): 0  EC: 2.4.2.6
UniProt
Find proteins for A0A3G5BRZ6 (Peribacillus psychrosaccharolyticus) Explore A0A3G5BRZ6  Go to UniProtKB:  A0A3G5BRZ6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.547	α = 90
b = 107.547	β = 90
c = 61.244	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Fresco-Tabohada, A., Fernandez-Lucas, J., Acebal, C., Arroyo, M., Ramon, F., Mancheno, J.M., de la Mata, I.

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description