4KZS | pdb_00004kzs

Crystal structure of the secreted protein HP1454 from the human pathogen Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb4KZS/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Helicobacter pylori R046Wa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2014-06-04 
• Deposition Author(s): Quarantini, S., Cendron, L., Fischer, W., Zanotti, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.304 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Literature

Crystal structure of the secreted protein HP1454 from the human pathogen Helicobacter pylori.

Quarantini, S., Cendron, L., Zanotti, G.

(2014) Proteins 82: 2868-2873

• PubMed: 24854568 
• DOI: https://doi.org/10.1002/prot.24608
• Primary Citation Related Structures: 
  4KZS


• PubMed Abstract: 
  

  HP1454 is a protein of 303 amino acids found in the extracellular milieu of Helicobacter pylori. The protein structure, crystallized in the orthorhombic C222₁ space group with one molecule per asymmetric unit, has been determined using the single-wavelength anomalous dispersion method. HP1454 exhibits an elongated bent shape, composed of three distinct domains. Each domain possesses a fold already present in other structures: Domain I contains a three-strand antiparallel β-barrel flanked by a long α-helix, Domain II is an anti-parallel three-helix bundle, and Domain III a β-sheet flanked by two α-helices. The overall assembly of the protein does not bear any similarity with known structures.

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Organizational Affiliation: 
• Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 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)

Macromolecule Content 

• Total Structure Weight: 32.26 kDa 
• Atom Count: 1,961 
• Modeled Residue Count: 242 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPP20 lipofamily protein	A	285	Helicobacter pylori R046Wa	Mutation(s): 0  Gene Names: hp1454, OUO_1490

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.304 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.64	α = 90
b = 101.35	β = 90
c = 121.08	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Quarantini, S., Cendron, L., Fischer, W., Zanotti, G.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations