1B79

N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB

• PDB DOI: https://doi.org/10.2210/pdb1B79/pdb

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


• Deposited: 1999-01-28 Released: 1999-06-30 
• Deposition Author(s): Fass, D., Bogden, C.E., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.263 

Literature

Crystal structure of the N-terminal domain of the DnaB hexameric helicase.

Fass, D., Bogden, C.E., Berger, J.M.

(1999) Structure 7: 691-698

• PubMed: 10404598 
• DOI: https://doi.org/10.1016/s0969-2126(99)80090-2
• Primary Citation of Related Structures:  
  1B79


• PubMed Abstract: 
  

  The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. Knowledge of the structure of this domain may contribute to an understanding of its role in DnaB function.

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Organizational Affiliation: 

Whitehead Institute, Cambridge, Massachusetts 02142, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.89 kDa 
• Atom Count: 3,245 
• Modelled Residue Count: 410 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaB Helicase	A, B, C, D	119	Escherichia coli	Mutation(s): 0  EC: 3.6.1
UniProt
Find proteins for P0ACB0 (Escherichia coli (strain K12)) Explore P0ACB0  Go to UniProtKB:  P0ACB0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.263 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.3	α = 90
b = 66.4	β = 93.8
c = 107	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-30 
Deposition Author(s): Fass, D., Bogden, C.E., Berger, J.M.

Revision History  

• Version 1.0: 1999-06-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-12-11
  Changes: Advisory, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references