9TCD | pdb_00009tcd

XFEL structure of oxidised Ribonucleotide reductase R2a Y122F mutant from E. coli, hexagonal P6122 form

• PDB DOI: https://doi.org/10.2210/pdb9TCD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2025-11-21 Released: 2026-05-13 
• Deposition Author(s): Kumar, R., Srinivas, V., Hogbom, M.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Tracking the redox reaction of the iron enzyme ribonucleotide reductase using continuous SerialED and SFX

Pacoste, L., Kumar, R., Srinivas, V., Makita, H., Simon, P.S., Bannerjee, R., Minnetian, N.M., Bhowmick, A., Paley, D.W., Mittan-Moreau, D.W., Chatterjee, K., Rosenberg, D.J., Batyuk, A., Gee, L.B., Alonso-Mori, R., Sauter, N.K., Yano, J., Yachandra, V.K., John, J., Aurelius, O., Brewster, A.S., Kern, J.F., Blomberg, B., Lebrette, H., Xu, H., Hofer, G., Hogbom, M., Zou, X.

(2026) Structure 

• DOI: https://doi.org/10.1016/j.str.2026.03.006

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.52 kDa 
• Atom Count: 2,822 
• Modeled Residue Count: 341 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase 1 subunit beta	A	375	Escherichia coli	Mutation(s): 1  Gene Names: nrdB, ftsB, b2235, JW2229 EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12)) Explore P69924  Go to UniProtKB:  P69924

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.508	α = 90
b = 93.508	β = 90
c = 203.591	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
cctbx.xfel	data reduction
cxi.merge	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-13 
Deposition Author(s): Kumar, R., Srinivas, V., Hogbom, M.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	2023.0201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM149528, GM110501, GM126289, GM117126, GM151988, R24GM154040
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515, DE-AC02-05CH11231

Revision History  

• Version 1.0: 2026-05-13
  Type: Initial release