4INN

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family.

Barison, N.Cendron, L.Loconte, V.Proctor, E.A.Dokholyan, N.V.Zanotti, G.

(2013) Acta Crystallogr.,Sect.D 69: 1387-1394

  • DOI: 10.1107/S0907444913008160

  • PubMed Abstract: 
  • Helicobacter pylori is a bacterial pathogen that causes severe diseases, including gastritis, ulcers and gastric cancer. Although this bacterium has been extensively studied, the physiological functions of a large number of the proteins encoded by it ...

    Helicobacter pylori is a bacterial pathogen that causes severe diseases, including gastritis, ulcers and gastric cancer. Although this bacterium has been extensively studied, the physiological functions of a large number of the proteins encoded by its genome are unknown. HP1028 is a protein that is relevant to colonization and to the survival of the bacterium in the stomach, but its function is not clearly understood. Bioinformatics studies suggest that HP1028 is a monomeric protein that is secreted in the H. pylori periplasm. The crystal structure of HP1028 has been determined at 2.6 Å resolution using the SAD method. The three-dimensional structure of the protein reveals that it belongs to the lipocalin family, a group of proteins that bind and transport (often hydrophobic) small molecules. The structure of HP1028, together with the possible localization of the mature protein in the bacterial periplasm and the position of the hp1028 gene in the bacterial genome, point to a role in H. pylori chemotaxis.


    Organizational Affiliation

    Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HP1028
A, B
178Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504Mutation(s): 1 
Find proteins for I0ZEL6 (Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504)
Go to UniProtKB:  I0ZEL6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download SDF File 
Download CCD File 
A
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
HEPTAETHYLENE GLYCOL, PEG330
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.240α = 90.00
b = 79.150β = 90.00
c = 131.670γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
ADSCdata collection
SHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references