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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 9G4R

Ligand Structure Quality Assessment

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

Literature

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

Huang, L., Lilley, D.M.J.

To be published.

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

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(by identity cutoff)

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.