5OK8

Crystal structure of protein Lpp20 (HP1456) from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb5OK8/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Helicobacter pylori J99
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-07-25 Released: 2017-12-06 
• Deposition Author(s): Zanotti, G., Mishra, N., Valesse, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.268 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

Helicobacter pylori antigenic Lpp20 is a structural homologue of Tip alpha and promotes epithelial-mesenchymal transition.

Vallese, F., Mishra, N.M., Pagliari, M., Berto, P., Codolo, G., de Bernard, M., Zanotti, G.

(2017) Biochim Biophys Acta 1861: 3263-3271

• PubMed: 28947343 
• DOI: https://doi.org/10.1016/j.bbagen.2017.09.017
• Primary Citation of Related Structures:  
  5OK8


• PubMed Abstract: 
  

  Helicobacter pylori is a bacterium that affects about 50% of the world population and, despite being often asymptomatic, it is responsible of several gastric diseases, from gastritis to gastric cancer. The protein Lpp20 (HP1456) plays an important role in bacterium survival and host colonization, but the possibility that it might be involved in the etiology of H. pylori-related disorders is an unexplored issue. Lpp20 is a lipoprotein bound to the external membrane of the bacterium, but it is also secreted inside vesicles along with other two proteins of the same operon, i.e. HP1454 and HP1457.

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Organizational Affiliation: 

Department of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35131, Italy.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

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: 76.84 kDa 
• Atom Count: 3,946 
• Modelled Residue Count: 457 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPP20 lipoprotein	A, B, C, D	175	Helicobacter pylori J99	Mutation(s): 0  Gene Names: lpp20, jhp_1349
UniProt
Find proteins for P0A0V1 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore P0A0V1  Go to UniProtKB:  P0A0V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.268 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.303	α = 90
b = 90.424	β = 90
c = 114.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Zanotti, G., Mishra, N., Valesse, F.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references