8XRG | pdb_00008xrg

The crystal structure of AsfvTopII ATPase domain in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb8XRG/pdb

• Classification: REPLICATION
• Organism(s): African swine fever virus BA71V
• Expression System: Escherichia coli
• 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: 1.61 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of AsfvTopII ATPase domain in complex with ADP

Yang, J., Gan, J.H.

(2024) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.01 kDa 
• Atom Count: 3,187 
• Modeled Residue Count: 393 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2	A	408	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.256	α = 90
b = 85.256	β = 90
c = 209.538	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	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