2VN2

Crystal structure of the N-terminal domain of DnaD protein from Geobacillus kaustophilus HTA426


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the N-Terminal Domain of Geobacillus Kaustophilus Hta426 Dnad Protein.

Huang, C.-Y.Chang, Y.-W.Chen, W.-T.

(2008) Biochem.Biophys.Res.Commun. 375: 220

  • DOI: 10.1016/j.bbrc.2008.07.160

  • PubMed Abstract: 
  • The DnaD is one of the primosomal proteins that are required for initiation and re-initiation of chromosomal DNA replication in Gram-positive bacteria. The DnaD protein is composed of two major structural domains: an N-terminal oligomerization domain ...

    The DnaD is one of the primosomal proteins that are required for initiation and re-initiation of chromosomal DNA replication in Gram-positive bacteria. The DnaD protein is composed of two major structural domains: an N-terminal oligomerization domain and a C-terminal ssDNA binding domain. Here, we report the crystal structure of the N-terminal domain (aa 1-128) of DnaD (DnaDn) of Geobacillus kaustophilus HTA426 at 2.3A resolution. The structure of DnaDn reveals an extended winged-helix fold, a typical double-stranded DNA binding motif as winged-helix proteins. DnaDn formed tetramers in the crystalline state, but the results of gel filtration chromatography further indicated that this domain of DnaD was a stable dimer in solution. The structural analysis of DnaDn may suggest the binding sites for DNA and DnaB, and an assembly mechanism for Gram-positive bacterial DNA replication primosome.


    Organizational Affiliation

    Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Road, Taichung 402, Taiwan. cyhuang@csmu.edu.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHROMOSOME REPLICATION INITIATION PROTEIN
A, B, C, D
128Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
Gene Names: dnaD
Find proteins for Q5KXY1 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KXY1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.217 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.514α = 90.00
b = 124.707β = 90.00
c = 157.230γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata reduction
SOLVEphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance