8JFR

N-terminal domain of AcrIIA15 in complex with palindromic DNA substrate

• PDB DOI: https://doi.org/10.2210/pdb8JFR/pdb
• NAKB: 8JFR

• Classification: VIRAL PROTEIN
• Organism(s): Staphylococcus delphini
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-18 Released: 2024-02-28 
• Deposition Author(s): Deng, X., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.259 
• R-Value Work: 0.246 
• R-Value Observed: 0.247 

Literature

N-terminal domain of AcrIIA15 in complex with palindromic DNA substrate

Deng, X., wang, Y.

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.68 kDa 
• Atom Count: 3,360 
• Modelled Residue Count: 322 
• Deposited Residue Count: 328 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIIA15	A [auth B], B [auth D], E [auth A], F [auth C]	63	Staphylococcus delphini	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*TP*GP*AP*CP*AP*AP*AP*TP*GP*TP*CP*AP*TP*AP*G)-3')	C [auth E], G	19	Staphylococcus delphini

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*AP*TP*GP*AP*CP*AP*TP*TP*TP*GP*TP*CP*AP*TP*AP*A)-3')	D [auth F], H	19	Staphylococcus delphini

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.259 
• R-Value Work: 0.246 
• R-Value Observed: 0.247 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.712	α = 90
b = 58.712	β = 90
c = 240.593	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Deng, X., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930065
National Natural Science Foundation of China (NSFC)	China	31725008

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release