4EVB | pdb_00004evb

Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)

• PDB DOI: https://doi.org/10.2210/pdb4EVB/pdb

• Classification: METAL TRANSPORT
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2012-06-27 
• Deposition Author(s): Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form

Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.

(2012) Biochem Biophys Res Commun 422: 745-750

• PubMed: 22618234 
• DOI: https://doi.org/10.1016/j.bbrc.2012.05.073


• PubMed Abstract: 
  

  Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn(2+)- or Cd(2+)-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Shizuoka 422-8526, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 19.62 kDa 
• Atom Count: 1,271 
• Modeled Residue Count: 143 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil-activating protein	A	164	Helicobacter pylori	Mutation(s): 0  Gene Names: napA
UniProt
Find proteins for G1UIZ3 (Helicobacter pylori) Explore G1UIZ3  Go to UniProtKB:  G1UIZ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.529	α = 90
b = 185.529	β = 90
c = 185.529	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description