2R6C

Crystal Form BH2

• PDB DOI: https://doi.org/10.2210/pdb2R6C/pdb

• Classification: REPLICATION
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-05 Released: 2008-06-10 
• Deposition Author(s): Bailey, S., Eliason, W.K., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.344 
• R-Value Work: 0.320 
• R-Value Observed: 0.321 

Literature

Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase

Bailey, S., Eliason, W.K., Steitz, T.A.

(2007) Science 318: 459-463

• PubMed: 17947583 
• DOI: https://doi.org/10.1126/science.1147353
• Primary Citation of Related Structures:  
  2R6A, 2R6C, 2R6D, 2R6E


• PubMed Abstract: 
  

  The complex between the DnaB helicase and the DnaG primase unwinds duplex DNA at the eubacterial replication fork and synthesizes the Okazaki RNA primers. The crystal structures of hexameric DnaB and its complex with the helicase binding domain (HBD) of DnaG reveal that within the hexamer the two domains of DnaB pack with strikingly different symmetries to form a distinct two-layered ring structure. Each of three bound HBDs stabilizes the DnaB hexamer in a conformation that may increase its processivity. Three positive, conserved electrostatic patches on the N-terminal domain of DnaB may also serve as a binding site for DNA and thereby guide the DNA to a DnaG active site.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 18-mer - A12B6 

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

Macromolecule Content

• Total Structure Weight: 354.59 kDa 
• Atom Count: 19,920 
• Modelled Residue Count: 2,562 
• Deposited Residue Count: 3,153 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicative helicase	A, B, C, D, E, F	454	N/A	Mutation(s): 0  Gene Names: DnaB, dnaB
UniProt
Find proteins for Q9X4C9 (Geobacillus stearothermophilus) Explore Q9X4C9  Go to UniProtKB:  Q9X4C9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaG Primase, Helicase Binding Domain	G, H, I	143	N/A	Mutation(s): 0  Gene Names: DnaG, dnaG EC: 2.7.7
UniProt
Find proteins for Q9X4D0 (Geobacillus stearothermophilus) Explore Q9X4D0  Go to UniProtKB:  Q9X4D0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	G, H, I	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.344 
• R-Value Work: 0.320 
• R-Value Observed: 0.321 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.775	α = 90
b = 228.775	β = 90
c = 192.984	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Bailey, S., Eliason, W.K., Steitz, T.A.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance