5HRK | pdb_00005hrk

The crystal structure of AsfvPolX(H115F mutant): 1nt-gap(P) DNA2:dGTP ternary complex

• PDB DOI: https://doi.org/10.2210/pdb5HRK/pdb
• NAKB: 5HRK

• Classification: TRANSFERASE/DNA
• Organism(s): African swine fever virus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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: 2.90 Å
• R-Value Free: 
  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.235 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.25 kDa 
• Atom Count: 4,167 
• Modeled Residue Count: 420 
• Deposited Residue Count: 426 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

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): 1  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(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3')	C [auth F], F [auth C]	9	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3')	D [auth H], G [auth E]	18	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3')	E [auth G], H [auth D]	8	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.273 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.726	α = 90
b = 87.196	β = 97.59
c = 82.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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: 2024-11-13
  Changes: Structure summary