9BJ5 | pdb_00009bj5

Crystal structure of the HEPN family member AbiV (P212121 space group)

• PDB DOI: https://doi.org/10.2210/pdb9BJ5/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Lactococcus cremoris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-25 Released: 2025-08-13 
• Deposition Author(s): Zhu, X., Moineau, S., Shi, R.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

HEPN-AbiV is an RNase in the AbiV antiphage system

Zhu, X., Morency, C., Picard, M.-E., Mosterd, C., McAlister, J.A., Perrault-Jolicoeur, A., Geddes-McAlister, J., Shi, R., Moineau, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 94.88 kDa 
• Atom Count: 4,823 
• Modeled Residue Count: 609 
• Deposited Residue Count: 828 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AbiV family abortive infection protein	A, D	207	Lactococcus cremoris	Mutation(s): 0
UniProt
Find proteins for A2RJ64 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RJ64  Go to UniProtKB:  A2RJ64

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AbiV family abortive infection protein	B	207	Lactococcus cremoris	Mutation(s): 0
UniProt
Find proteins for A2RJ64 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RJ64  Go to UniProtKB:  A2RJ64

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AbiV family abortive infection protein	C	207	Lactococcus cremoris	Mutation(s): 0
UniProt
Find proteins for A2RJ64 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RJ64  Go to UniProtKB:  A2RJ64

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.693	α = 90
b = 79.168	β = 90
c = 136.137	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Zhu, X., Moineau, S., Shi, R.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	436202

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release