5LNL | pdb_00005lnl

Crystal structure of Hsf 1608-1749 putative domain 1

• PDB DOI: https://doi.org/10.2210/pdb5LNL/pdb

• Classification: CELL ADHESION
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-05 Released: 2017-02-15 
• Deposition Author(s): Thomsen, M., Wright, J., Ridley, J., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.334 (Depositor), 0.331 (DCC) 
• R-Value Work: 
  0.296 (Depositor), 0.302 (DCC) 

Starting Model: experimental

Literature

The crystal structure of PD1, a Haemophilus surface fibril domain.

Wright, J., Thomsen, M., Kolodziejczyk, R., Ridley, J., Sinclair, J., Carrington, G., Singh, B., Riesbeck, K., Goldman, A.

(2017) Acta Crystallogr F Struct Biol Commun 73: 101-108

• PubMed: 28177321 
• DOI: https://doi.org/10.1107/S2053230X17001406
• Primary Citation Related Structures: 
  5LNL


• PubMed Abstract: 
  

  The Haemophilus surface fibril (Hsf) is an unusually large trimeric autotransporter adhesin (TAA) expressed by the most virulent strains of H. influenzae. Hsf is known to mediate adhesion between pathogen and host, allowing the establishment of potentially deadly diseases such as epiglottitis, meningitis and pneumonia. While recent research has suggested that this TAA might adopt a novel `hairpin-like' architecture, the characterization of Hsf has been limited to in silico modelling and electron micrographs, with no high-resolution structural data available. Here, the crystal structure of Hsf putative domain 1 (PD1) is reported at 3.3 Å resolution. The structure corrects the previous domain annotation by revealing the presence of an unexpected N-terminal TrpRing domain. PD1 represents the first Hsf domain to be solved, and thus paves the way for further research on the `hairpin-like' hypothesis.

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Organizational Affiliation: 
• Astbury Centre for Structural Molecular Biology, School of Biomedical Science, University of Leeds, Leeds LS2 9JT, England.
Department of Clinical Microbiology, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 143.64 kDa 
• Atom Count: 8,073 
• Modeled Residue Count: 1,178 
• Deposited Residue Count: 1,359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hsf	A, B, C, D, E, F, G, H, I	151	Haemophilus influenzae	Mutation(s): 0  Gene Names: hsf
UniProt
Find proteins for P71401 (Haemophilus influenzae) Explore P71401  Go to UniProtKB:  P71401

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.334 (Depositor), 0.331 (DCC) 
• R-Value Work:  0.296 (Depositor), 0.302 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.438	α = 90
b = 50.4	β = 101.94
c = 256.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Thomsen, M., Wright, J., Ridley, J., Goldman, A.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description