9LQH | pdb_00009lqh

Crystal structure of SAM lyase in complex with sinefungin-AMP

• PDB DOI: https://doi.org/10.2210/pdb9LQH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Clostridium botulinum A str. Hall
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-28 Released: 2025-11-26 
• Deposition Author(s): Duan, B., Zhao, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: in silico

Literature

Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.

Duan, B., Zhao, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.09 kDa 
• Atom Count: 3,535 
• Modeled Residue Count: 371 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM lyase	A, B, C	125	Clostridium botulinum A str. Hall	Mutation(s): 0  Gene Names: CBO2178
UniProt
Find proteins for A5I3U9 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore A5I3U9  Go to UniProtKB:  A5I3U9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EL1 (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	(2~{S},5~{S})-6-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]-2,5-bis(azanyl)hexanoic acid C25 H35 N12 O11 P XNBPELUUEBZQEC-PYTRVWNWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.16	α = 90
b = 53.88	β = 90
c = 153.37	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Duan, B., Zhao, B.

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

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release