2VN2

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

• PDB DOI: https://doi.org/10.2210/pdb2VN2/pdb

• Classification: REPLICATION
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-30 Released: 2008-08-12 
• Deposition Author(s): Huang, C.-Y., Chang, Y.-W., Chen, W.-T., Sun, Y.-J., Hsiao, C.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

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

• PubMed: 18703019 
• DOI: https://doi.org/10.1016/j.bbrc.2008.07.160
• Primary Citation of Related Structures:  
  2VN2


• 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 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.

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Organizational Affiliation: 

Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien-Kuo N. Road, Taichung 402, Taiwan. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.64 kDa 
• Atom Count: 3,650 
• Modelled Residue Count: 443 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHROMOSOME REPLICATION INITIATION PROTEIN	A, B, C, D	128	Geobacillus kaustophilus HTA426	Mutation(s): 0
UniProt
Find proteins for Q5KXY1 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KXY1  Go to UniProtKB:  Q5KXY1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.514	α = 90
b = 124.707	β = 90
c = 157.23	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Huang, C.-Y., Chang, Y.-W., Chen, W.-T., Sun, Y.-J., Hsiao, C.-D.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other