9IR2 | pdb_00009ir2

phage HY126 hydroxylase AfhB with cofactor FMN and substrate dCMP

• PDB DOI: https://doi.org/10.2210/pdb9IR2/pdb

• Classification: HYDROLASE
• Organism(s): Phage #D
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2024-07-13 Released: 2025-07-16 
• Deposition Author(s): Yu, H., Lianrong, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: in silico

Literature

STRUCTURE of protein XAN60475 at 1.31 angstroms resolution

Yu, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.09 kDa 
• Atom Count: 2,243 
• Modeled Residue Count: 234 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	238	Phage #D	Mutation(s): 0  Gene Names: 308Ecol101PP_00194
UniProt
Find proteins for Q7Y590 (Escherichia phage RB69) Explore Q7Y590  Go to UniProtKB:  Q7Y590

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
DCM (Subject of Investigation/LOI)	C [auth A]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N
GOL (Subject of Investigation/LOI)	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.6	α = 90
b = 64.6	β = 90
c = 230.21	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Yu, H., Lianrong, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release