6JDE

crystal structure of a DNA repair protein

• PDB DOI: https://doi.org/10.2210/pdb6JDE/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-02-01 Released: 2019-06-26 
• Deposition Author(s): Yan, X.X., Tang, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Literature

Crystal structure of a novel ATPase RadD from Escherichia coli.

Kuang, X., Tang, Q., Liu, Y.P., Yan, X.X., Xu, W.

(2019) Proteins 87: 791-795

• PubMed: 31035307 
• DOI: https://doi.org/10.1002/prot.25704
• Primary Citation of Related Structures:  
  6JDE


• PubMed Abstract: 
  

  The helicase superfamily 2 (SF2) proteins are involved in essentially every step in DNA and RNA metabolism. The radD (yejH) gene, which belongs to SF2, plays an important role in DNA repair. The RadD protein includes all seven conserved SF2 motifs and has shown ATPase activity. Here, we first reported the structure of RadD from Escherichia coli containing two RecA-like domains, a zinc finger motif, and a C-terminal domain. Based on the structure of RadD and other SF2 proteins, we then built a model of the RedD-ATP complex.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 133.15 kDa 
• Atom Count: 9,030 
• Modelled Residue Count: 1,127 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA repair helicase RadD	A [auth B], B [auth A]	586	Escherichia coli K-12	Mutation(s): 0  Gene Names: radD, yejH, yejI, yejJ, b2184, JW2172 EC: 3.6.4.12
UniProt
Find proteins for P33919 (Escherichia coli (strain K12)) Explore P33919  Go to UniProtKB:  P33919

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.240 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.515	α = 90
b = 78.455	β = 98.5
c = 110.587	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Yan, X.X., Tang, Q.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Advisory, Data collection, Database references