3TA8

Crystal structure HP-NAP from strain YS39 iron loaded (cocrystallization 5mM)

• PDB DOI: https://doi.org/10.2210/pdb3TA8/pdb

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


• Deposited: 2011-08-03 Released: 2012-02-08 
• Deposition Author(s): Tsuruta, O., Yokoyama, H., Fujii, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)

Tsuruta, O., Yokoyama, H., Fujii, S.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 134-140

• PubMed: 22297984 
• DOI: https://doi.org/10.1107/S1744309111052675
• Primary Citation of Related Structures:  
  3T9J, 3TA8


• PubMed Abstract: 
  

  A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP) has been determined in two forms: the native state (Apo) at 2.20 Å resolution and an iron-loaded form (Fe-load) at 2.50 Å resolution. The highly solvated packing of the dodecameric shell is suitable for crystallographic study of the metal ion-uptake pathway. Like other bacterioferritins, HP-NAP forms a spherical dodecamer with 23 symmetry including two kinds of channels. Iron loading causes a series of conformational changes of amino-acid residues (Trp26, Asp52 and Glu56) at the ferroxidase centre.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, University of Shizuoka, Suruga-ku, Shizuoka-shi, Shizuoka, Japan.

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: 19.37 kDa 
• Atom Count: 1,276 
• Modelled Residue Count: 144 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.53	α = 90
b = 188.53	β = 90
c = 188.53	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Tsuruta, O., Yokoyama, H., Fujii, S.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description