5HRE | pdb_00005hre

The crystal structure of AsfvPolX:DNA3 binary complex

• PDB DOI: https://doi.org/10.2210/pdb5HRE/pdb
• NAKB: 5HRE

• 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: 1.75 Å
• R-Value Free: 
  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.66 kDa 
• Atom Count: 1,725 
• Modeled Residue Count: 185 
• Deposited Residue Count: 187 
• 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	178	African swine fever virus	Mutation(s): 0  Gene Names: O174L EC: 2.7.7.7
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(P*AP*GP*GP*AP*TP*CP*CP*T)-3')	B	9	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.144	α = 90
b = 88.785	β = 94.61
c = 43.349	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, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary