5HRD

The crystal structure of AsfvPolX:DNA2 binary complex

• PDB DOI: https://doi.org/10.2210/pdb5HRD/pdb
• NAKB: 5HRD

• Classification: TRANSFERASE/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-23 Released: 2017-01-18 
• Deposition Author(s): Chen, Y.Q., Zhang, J., Gan, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1

Chen, Y.Q., Zhang, J., Gan, J.H.

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 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: 92.89 kDa 
• Atom Count: 6,687 
• Modelled Residue Count: 738 
• Deposited Residue Count: 744 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta-like protein	A, B, C, D	178	African swine fever virus	Mutation(s): 0  Gene Names: O174L
UniProt
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted)) Explore P42494  Go to UniProtKB:  P42494

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*G)-3')	E, F, G, H	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth A], K [auth B], L [auth C], M [auth D], N [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.196	α = 90
b = 87.485	β = 91.45
c = 87.914	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Chen, Y.Q., Zhang, J., Gan, J.H.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description