8XRI | pdb_00008xri

The crystal structure of AsfvTopII in complex with both G-DNA and T-DNA

• PDB DOI: https://doi.org/10.2210/pdb8XRI/pdb
• NAKB: 8XRI

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of AsfvTopII in complex with both G-DNA and T-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: 215.37 kDa 
• Atom Count: 14,259 
• Modeled Residue Count: 1,640 
• Deposited Residue Count: 1,680 
• 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 (56-MER)	C, D [auth E], E [auth G], F [auth H]	28	African swine fever virus BA71V

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD (Subject of Investigation/LOI)	J [auth A], M [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.21	α = 90
b = 134.366	β = 90
c = 135.926	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	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.

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

Revision History  

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