9KJA | pdb_00009kja

Anti-CRISPR protein AcrVA3

• PDB DOI: https://doi.org/10.2210/pdb9KJA/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Neisseria sp. HMSC056A03
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-12 Released: 2025-11-12 
• Deposition Author(s): Han, J.H., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: in silico

Literature

AcrVA3 is an anti-CRISPR protein that acts on DNA to inhibit Cas12a.

Han, J.H., Park, H.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 12.76 kDa 
• Atom Count: 647 
• Modeled Residue Count: 69 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HNH endonuclease	A	111	Neisseria sp. HMSC056A03	Mutation(s): 0  Gene Names: HMPREF3052_01670

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.9	α = 90
b = 44.9	β = 90
c = 47.34	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Han, J.H., Park, H.H.

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release