6EVS | pdb_00006evs

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 (Depositor), 0.217 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 274
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.217 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.