Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 12.01 kDa 
• Atom Count: 952 
• Residue Count: 109 
• Unique protein chains: 1

5OMT

Endonuclease NucB

• DOI: 10.2210/pdb5OMT/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus licheniformis
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2017-08-01 Released: 2017-11-15 
• Deposition Author(s): Basle, A., Lewis, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.186 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Literature

Crystal structure of NucB, a biofilm-degrading endonuclease.

Basle, A., Hewitt, L., Koh, A., Lamb, H.K., Thompson, P., Burgess, J.G., Hall, M.J., Hawkins, A.R., Murray, H., Lewis, R.J.

(2018) Nucleic Acids Res 46: 473-484

• PubMed: 29165717 
• DOI: 10.1093/nar/gkx1170
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NucB	A	110	Bacillus licheniformis	Mutation(s): 0  Gene Names: nucB
Find proteins for F1BV52 (Bacillus licheniformis) Go to UniProtKB:  F1BV52

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.186 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.955	α = 90
b = 59.955	β = 90
c = 66.604	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
Aimless	data scaling
SHELXCD	phasing
SHELXE	model building
ARP/wARP	model building
BUCCANEER	model building
REFMAC	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-08-01 
• Released Date: 2017-11-15 
Deposition Author(s): Basle, A., Lewis, R.J.

Revision History 

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Database references