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.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3G5BRZ6
Sequence Annotations Expand
Reference Sequence

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

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Entry History

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Fresco-Tabohada, A.

Fernandez-Lucas, J.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.