9GN4

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Y7F/D72N mutant with cytidine

PDB DOI: https://doi.org/10.2210/pdb9GN4/pdb

Classification: TRANSFERASE
Organism(s): Lactobacillus leichmannii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-30 Released: 2024-12-25
Deposition Author(s): Ascham, A., Salihovic, A., Burley, G., Grogan, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.188
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2

Salihovic, A., Ascham, A., Rosenqvist, P.S., Taladriz-Sender, A., Hoskisson, P.A., Hodgson, D.R.W., Grogan, G., Burley, G.A.

(2024) Chem Sci

DOI: https://doi.org/10.1039/d4sc07521h

Macromolecule Content

Total Structure Weight: 36.65 kDa
Atom Count: 2,663
Modelled Residue Count: 314
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B	157	Lactobacillus leichmannii	Mutation(s): 2 Gene Names: ntd EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii) Explore Q9R5V5 Go to UniProtKB: Q9R5V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R5V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTN (Subject of Investigation/LOI) Query on CTN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.188
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.134	α = 90
b = 150.134	β = 90
c = 150.134	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-12-25
Type: Initial release

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.