1JI4

NAP protein from helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Neutrophil-activating Protein from Helicobacter pylori

Zanotti, G.Papinutto, E.Dundon, W.G.Battistutta, R.Seveso, M.Del Giudice, G.Rappuoli, R.Montecucco, C.

(2002) J.Mol.Biol. 323: 125-130

  • Also Cited By: 2FJC, 1O9R

  • PubMed Abstract: 
  • Helicobacter pylori is a major human pathogen associated with severe gastroduodenal diseases, including ulcers and cancers. An H.pylori protein that is highly immunogenic in humans and mice has been identified recently. This protein has been termed H ...

    Helicobacter pylori is a major human pathogen associated with severe gastroduodenal diseases, including ulcers and cancers. An H.pylori protein that is highly immunogenic in humans and mice has been identified recently. This protein has been termed HP-NAP, due to its ability of activating neutrophils. In order to achieve a molecular understanding of its unique immunogenic and pro-inflammatory properties, we have determined its three-dimensional structure. Its quaternary structure is similar to that of the dodecameric bacterial ferritins (Dps-like family), but it has a different surface potential charge distribution. This is due to the presence of a large number of positively charged residues, which could well account for its unique ability in activating human leukocytes.


    Related Citations: 
    • The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron Binding Site
      Ilari, A.,Stefanini, S.,Chiancone, E.,Tsernoglou, D.
      (2000) Nat.Struct.Mol.Biol. 7: 38
    • The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
      Grant, R.A.,Filman, D.J.,Finkel, S.E.,Kolter, R.,Hogle, J.M.
      (1998) Nat.Struct.Mol.Biol. 5: 294


    Organizational Affiliation

    Dipartimento di Chimica Organica e Centro CNR Biopolimeri, Università di Padova, Via Marzolo 1, 35131, Padova, Italy. giuseppe.zanotti@unipd.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL-ACTIVATING PROTEIN A
A, B, C, D, E, F, G, H, I, J, K, L
144Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: dps (napA)
EC: 1.16.-.-
Find proteins for P43313 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P43313
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.778α = 90.00
b = 133.225β = 93.99
c = 95.228γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance