4D40

High-Resolution Structure of a Type IV Pilin from Shewanella oneidensis

• PDB DOI: https://doi.org/10.2210/pdb4D40/pdb

• Classification: CELL ADHESION
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-24 Released: 2015-04-29 
• Deposition Author(s): Gorgel, M., JensenUlstrup, J., Boeggild, A., Nissen, P., Boesen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.207 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

High-Resolution Structure of a Type Iv Pilin from the Metal- Reducing Bacterium Shewanella Oneidensis.

Gorgel, M., Ulstrup, J.J., Boggild, A., Jones, N.C., Hoffmann, S.V., Nissen, P., Boesen, T.

(2015) BMC Struct Biol 15: 4

• PubMed: 25886849 
• DOI: https://doi.org/10.1186/s12900-015-0031-7
• Primary Citation of Related Structures:  
  4D40, 4US7


• PubMed Abstract: 
  

  Type IV pili are widely expressed among Gram-negative bacteria, where they are involved in biofilm formation, serve in the transfer of DNA, motility and in the bacterial attachment to various surfaces. Type IV pili in Shewanella oneidensis are also supposed to play an important role in extracellular electron transfer by the attachment to sediments containing electron acceptors and potentially forming conductive nanowires.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, Aarhus C, 8000, Denmark. [e-mail].

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)

Macromolecule Content

• Total Structure Weight: 19.95 kDa 
• Atom Count: 1,631 
• Modelled Residue Count: 178 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PILD PROCESSED PROTEIN	A, B	89	Shewanella oneidensis MR-1	Mutation(s): 0
UniProt
Find proteins for Q8EII5 (Shewanella oneidensis (strain MR-1)) Explore Q8EII5  Go to UniProtKB:  Q8EII5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.207 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.91	α = 90
b = 96.46	β = 90
c = 110.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Gorgel, M., JensenUlstrup, J., Boeggild, A., Nissen, P., Boesen, T.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description