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.

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33919
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Yan, X.X.

Tang, Q.

Revision History (Full details and data files)

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