5J4G | pdb_00005j4g

Crystal structure of the C-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori

Sim, D.W.Kim, J.H.Kim, H.Y.Jang, J.H.Lee, W.C.Kim, E.H.Park, P.J.Lee, K.H.Won, H.S.

(2016) FEBS Lett 590: 2997-3004

  • DOI: https://doi.org/10.1002/1873-3468.12332
  • Primary Citation Related Structures: 
    5J4F, 5J4G

  • PubMed Abstract: 

    We solved the crystal structure of a functionally uncharacterized protein, HP0902, from Helicobacter pylori. Its structure demonstrated an all-β cupin fold that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. In contrast, isothermal titration calorimetry and NMR titration demonstrated that HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins. This report constitutes the first identification of an LPS-interacting protein, both in the cupin family and in H. pylori. Furthermore, identification of the ability of HP0902 to bind LPS uncovers a putative role for this protein in H. pylori pathogenicity.


  • Organizational Affiliation
    • Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea.

Macromolecule Content 

  • Total Structure Weight: 24.24 kDa 
  • Atom Count: 1,554 
  • Modeled Residue Count: 196 
  • Deposited Residue Count: 214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
107Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0902
UniProt
Find proteins for O25562 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25562 
Go to UniProtKB:  O25562
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25562
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.355α = 90
b = 50.355β = 90
c = 142.031γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata processing
SCALAdata scaling
MOLREPphasing
SHELXDEmodel building
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description