9LQC | pdb_00009lqc

Crystal structure of NrN D119A in complex with SAH-AMP

• PDB DOI: https://doi.org/10.2210/pdb9LQC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.37 Å
• R-Value Free: 
  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.257 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 122.68 kDa 
• Atom Count: 8,803 
• Modeled Residue Count: 1,004 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrN	A, B, C, D	260	Bacteroides fragilis	Mutation(s): 1  Gene Names: CQW34_02202, F2Z29_06630, F2Z89_11900, F3B44_04915, FSA03_20595, NXX45_16660
UniProt
Find proteins for A0A2M9V7I2 (Bacteroides fragilis) Explore A0A2M9V7I2  Go to UniProtKB:  A0A2M9V7I2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EL0 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(2~{S})-4-[[(2~{S},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]methylsulfanyl]-2-azanyl-butanoic acid C24 H32 N11 O11 P S QBCXMARFZQJLMA-XPJWLEQASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.668	α = 90
b = 121.609	β = 90.31
c = 72.579	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	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