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

  • DOI: 10.1016/s0022-2836(02)00879-3
  • Primary Citation of Related Structures:  
    1JI4

  • 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 HP-NAP, due to its ability of activating neutrophils ...

    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 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 Biol 5: 294
    • The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron Binding Site
      Ilari, A., Stefanini, S., Chiancone, E., Tsernoglou, D.
      (2000) Nat Struct Biol 7: 38

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUTROPHIL-ACTIVATING PROTEIN A
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
144Helicobacter pyloriMutation(s): 0 
Gene Names: napA
EC: 1.16
UniProt
Find proteins for P43313 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P43313 
Go to UniProtKB:  P43313
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth E] , DA [auth F] , GA [auth G] , JA [auth H] , MA [auth I] , O [auth A] , PA [auth J] , R [auth B] , 
AA [auth E],  DA [auth F],  GA [auth G],  JA [auth H],  MA [auth I],  O [auth A],  PA [auth J],  R [auth B],  SA [auth K],  U [auth C],  VA [auth L],  X [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
BA [auth F] , EA [auth G] , HA [auth H] , KA [auth I] , M [auth A] , NA [auth J] , P [auth B] , QA [auth K] , 
BA [auth F],  EA [auth G],  HA [auth H],  KA [auth I],  M [auth A],  NA [auth J],  P [auth B],  QA [auth K],  S [auth C],  TA [auth L],  V [auth D],  Y [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
CA [auth F] , FA [auth G] , IA [auth H] , LA [auth I] , N [auth A] , OA [auth J] , Q [auth B] , RA [auth K] , 
CA [auth F],  FA [auth G],  IA [auth H],  LA [auth I],  N [auth A],  OA [auth J],  Q [auth B],  RA [auth K],  T [auth C],  UA [auth L],  W [auth D],  Z [auth E]
UNKNOWN ATOM OR ION
X
 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
b = 133.225β = 93.99
c = 95.228γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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