8KEN | pdb_00008ken

Structure of DexA reveal the novel mechanism of DNA catalysis

• PDB DOI: https://doi.org/10.2210/pdb8KEN/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia phage EcSzw_1
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S
• Mutation(s): No 


• Deposited: 2023-08-12 Released: 2025-02-19 
• Deposition Author(s): Liu, Y.H., Ma, B., Kang, Y., Liu, B., Li, Y.
• Funding Organization(s): China Postdoctoral Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: other

Literature

The crystal structure of M-EXOD

Liu, Y.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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.87 kDa 
• Atom Count: 3,481 
• Modeled Residue Count: 448 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease	A [auth B], B [auth A]	227	Escherichia phage EcSzw_1	Mutation(s): 0  Gene Names: dexA EC: 3.1.11.1
UniProt
Find proteins for P04536 (Enterobacteria phage T4) Explore P04536  Go to UniProtKB:  P04536

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.33	α = 90
b = 82.182	β = 90
c = 115.931	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Liu, Y.H., Ma, B., Kang, Y., Liu, B., Li, Y.

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Funding Organization	Location	Grant Number
China Postdoctoral Science Foundation	China	2020M682420

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release