9XAL | pdb_00009xal

Crystal structure of RhoBAST-G38A in complex of TMR-DN

• PDB DOI: https://doi.org/10.2210/pdb9XAL/pdb

• Classification: RNA
• Organism(s): synthetic construct
• Expression System: in vitro transcription vector pT7-TP(deltai)
• Mutation(s): No 


• Deposited: 2025-10-22 Released: 2026-10-28 
• Deposition Author(s): Tai, X.Q., Ren, A.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RhoBAST-G38A in complex of TMR-DN

Tai, X.Q., Ren, A.M.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 19.23 kDa 
• Atom Count: 1,293 
• Modeled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (57-MER)	A [auth B]	57	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EZE( Subject of Investigation/LOI)	B	[9-[2-carboxy-4-[2-[2-[2-[(2,4-dinitrophenyl)amino]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C37 H39 N6 O10 XJJZEOMXQMSRAG-UHFFFAOYSA-O
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.267 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.987	α = 90
b = 83.987	β = 90
c = 106.718	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Tai, X.Q., Ren, A.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release