8XRF | pdb_00008xrf

The crystal structure of AsfvTopII in complex with G-DNA

• PDB DOI: https://doi.org/10.2210/pdb8XRF/pdb
• NAKB: 8XRF

• Classification: REPLICATION
• Organism(s): African swine fever virus BA71V
• Expression System: Escherichia coli, chemical production metagenome
• Mutation(s): No 


• Deposited: 2024-01-07 Released: 2024-08-07 
• Deposition Author(s): Yang, J., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of AsfvTopII in complex with G-DNA

Yang, J., Gan, J.H.

(2024) Nat Commun 

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 244.78 kDa 
• Atom Count: 13,390 
• Modeled Residue Count: 1,598 
• Deposited Residue Count: 1,776 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2	A, B	784	African swine fever virus BA71V	Mutation(s): 0  Gene Names: TOP, Ba71V-112, P1192R EC: 5.6.2.2
UniProt
Find proteins for Q00942 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore Q00942  Go to UniProtKB:  Q00942

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (52-MER)	C, D, E, F	52	African swine fever virus BA71V

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.77	α = 90
b = 126.41	β = 90
c = 135.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Yang, J., Gan, J.H.

---

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

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release