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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of M-EXOD

Liu, Y.H.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04536
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.