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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Han, J.H., Park, H.H.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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

View Full Validation Report

View more in-depth experimental data

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 (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.