22MX | pdb_000022mx

Crystal structure of a variant c-di-GMP-II Riboswitch c-di-GMP-II-Bh_A9G/U55C bound with 2',3'-cGAMP

• PDB DOI: https://doi.org/10.2210/pdb22MX/pdb

• Classification: RNA
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: in vitro transcription vector pT7-TP(deltai)
• Mutation(s): Yes 


• Deposited: 2026-01-16 Released: 2026-10-21 
• Deposition Author(s): Xu, X.C., 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: 2.90 Å
• R-Value Free: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a variant c-di-GMP-II Riboswitch BhP1-5delC A9G/U55C bound with 2',3'-cGAMP

Xu, X.C., Ren, A.M.

To be published.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.44 kDa 
• Atom Count: 3,413 
• Modeled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (77-MER)	A, B	77	Halalkalibacterium halodurans C-125

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1SY (Subject of Investigation/LOI)	C [auth A], F [auth B]	cGAMP C20 H24 N10 O13 P2 XRILCFTWUCUKJR-INFSMZHSSA-N
MG	D [auth A], E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.228	α = 90
b = 93.228	β = 90
c = 102.372	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: 2026-10-21 
Deposition Author(s): Xu, X.C., 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: 2026-10-21
  Type: Initial release