8JDH

Crystal structure of anti-CRISPR AcrIF25

• PDB DOI: https://doi.org/10.2210/pdb8JDH/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Alcanivorax sp. KX64203
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-14 Released: 2024-05-29 
• Deposition Author(s): Yang, J., Wang, J., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.192 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

An anti-CRISPR that pulls apart a CRISPR-Cas complex

Trost, C.N., Yang, J., Garcia, B., Hidalgo-Reyes, Y., Fung, B.C.M., Wang, J., Lu, W.T., Maxwell, K.L., Wang, Y., Davidson, A.R.

(2024) Nature 632: 375-382

• DOI: https://doi.org/10.1038/s41586-024-07642-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.78 kDa 
• Atom Count: 2,509 
• Modelled Residue Count: 295 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIF25	A, B	166	Alcanivorax sp. KX64203	Mutation(s): 0  Gene Names: A3Q32_18550

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.192 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.953	α = 90
b = 52.289	β = 105.91
c = 85.121	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
HKL-3000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Yang, J., Wang, J., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91940302
National Natural Science Foundation of China (NSFC)	China	31725008

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Database references
• Version 1.2: 2024-08-21
  Changes: Database references
• Version 1.3: 2024-09-04
  Changes: Database references