9EMX | pdb_00009emx

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Double Mutant Y7F A9S bound to Cordycepin

• PDB DOI: https://doi.org/10.2210/pdb9EMX/pdb

• Classification: TRANSFERASE
• Organism(s): Chroococcidiopsis thermalis PCC 7203
• Expression System: Escherichia coli B
• Mutation(s): Yes 


• Deposited: 2024-03-11 Released: 2025-05-07 
• Deposition Author(s): Tang, P., Harding, C.J., Czekster, C.M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Models: experimental

Literature

Engineered nucleoside 2'-deoxyribonsyltransferase enzymes enable scalable synthesis of diverse nucleoside analogues

Tang, P., Harding, C.J., Czekster, C.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.76 kDa 
• Atom Count: 5,488 
• Modeled Residue Count: 612 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside 2-deoxyribosyltransferase	A, B, C, D	154	Chroococcidiopsis thermalis PCC 7203	Mutation(s): 2  Gene Names: Chro_1188
UniProt
Find proteins for K9TVX3 (Chroococcidiopsis thermalis (strain PCC 7203)) Explore K9TVX3  Go to UniProtKB:  K9TVX3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3AD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	3'-DEOXYADENOSINE C10 H13 N5 O3 OFEZSBMBBKLLBJ-BAJZRUMYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.38	α = 90
b = 97.38	β = 90
c = 66.456	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Tang, P., Harding, C.J., Czekster, C.M.

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Funding Organization	Location	Grant Number
Other private	United Kingdom	IBioIC 2020-2-1

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 2.0: 2025-08-06
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary