5HRF | pdb_00005hrf

The crystal structure of AsfvPolX: DNA5: dGTP ternary complex

• PDB DOI: https://doi.org/10.2210/pdb5HRF/pdb
• NAKB: 5HRF

• Classification: TRANSFERASE/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli
• 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: 2.25 Å
• R-Value Free: 
  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

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: 47.97 kDa 
• Atom Count: 3,274 
• Modeled Residue Count: 370 
• Deposited Residue Count: 374 
• 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	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(*CP*AP*GP*GP*AP*TP*CP*CP*T*)-3')	C, D	9	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	F [auth A], I [auth B]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
SO4	H [auth B], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.706	α = 90
b = 75.441	β = 90
c = 108.45	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: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description