9G4R | pdb_00009g4r

Crystal structure of the DUF2693-FD RNA motif

• PDB DOI: https://doi.org/10.2210/pdb9G4R/pdb
• NAKB: 9G4R

• Classification: RNA
• Organism(s): Phocaeicola dorei CL03T12C01
• Mutation(s): No 


• Deposited: 2024-07-16 Released: 2025-07-30 
• Deposition Author(s): Huang, L., Lilley, D.M.J.
• Funding Organization(s): Cancer Research UK, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Structural basis for tRNA-mimicking by DUF2693-FD RNA motif

Huang, L., Lilley, D.M.J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 15.58 kDa 
• Atom Count: 1,027 
• Modeled Residue Count: 47 
• Deposited Residue Count: 47 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (47-MER)	A	47	Phocaeicola dorei CL03T12C01

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA (Subject of Investigation/LOI)	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.761	α = 90
b = 110.761	β = 90
c = 74.784	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Huang, L., Lilley, D.M.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	A18604
National Natural Science Foundation of China (NSFC)	China	32171191

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release