8KEL | pdb_00008kel

Structure of DexA reveal the novel Mechanism of DNA catalysis

• PDB DOI: https://doi.org/10.2210/pdb8KEL/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli 0.1197
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• 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): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: other

Literature

Structure of EXOD at 2.4 Angstroms resolution

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.

Biological Assembly Evidence: gel filtration

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: 103.98 kDa 
• Atom Count: 6,550 
• Modeled Residue Count: 853 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease	A, B, C, D	227	Escherichia coli 0.1197	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: 2.88 Å
• R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.548	α = 90
b = 76.285	β = 93.36
c = 108.009	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
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
National Natural Science Foundation of China (NSFC)	China	82172299

Revision History  

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