9LQA | pdb_00009lqa

Crystal structure of NrN E21A in complex with SAM-AMP

• PDB DOI: https://doi.org/10.2210/pdb9LQA/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: 1.91 Å
• R-Value Free: 
  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.199 (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

Macromolecule Content 

• Total Structure Weight: 30.85 kDa 
• Atom Count: 2,301 
• Modeled Residue Count: 251 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NrN	A	260	Bacteroides fragilis	Mutation(s): 1  Gene Names: CQW34_02202
UniProt
Find proteins for A0A2M9V7I2 (Bacteroides fragilis) Explore A0A2M9V7I2  Go to UniProtKB:  A0A2M9V7I2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EL3 (Subject of Investigation/LOI)	B [auth A]	[(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]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium C25 H35 N11 O11 P S AKDVTEPPXUCZRD-YBZFFHRHSA-O
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.396	α = 90
b = 71.396	β = 90
c = 121.502	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
DIALS	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