1JI4 | pdb_00001ji4

NAP protein from helicobacter pylori

PDB DOI: https://doi.org/10.2210/pdb1JI4/pdb

Classification: METAL TRANSPORT
Organism(s): Helicobacter pylori
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2001-06-29 Released: 2002-10-09
Deposition Author(s): Zanotti, G., Papinutto, E., Dundon, W.G., Battistutta, R., Seveso, M., Del Giudice, G., Rappuoli, R., Montecucco, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.224 (Depositor), 0.225 (DCC)
R-Value Work:
0.215 (Depositor), 0.217 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 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 Biology 323: 125-130

PubMed: 12368104 Search on PubMed
DOI: https://doi.org/10.1016/s0022-2836(02)00879-3
Primary Citation 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. 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 205.61 kDa
Atom Count: 15,118
Modeled Residue Count: 1,728
Deposited Residue Count: 1,728
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL-ACTIVATING PROTEIN A	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	144	Helicobacter pylori	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43313
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain VA [auth L] SDF format, chain U [auth C] SDF format, chain SA [auth K] SDF format, chain R [auth B] SDF format, chain PA [auth J] SDF format, chain O [auth A] SDF format, chain MA [auth I] SDF format, chain JA [auth H] SDF format, chain GA [auth G] SDF format, chain DA [auth F] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain VA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain VA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth F] GA [auth G] JA [auth H] MA [auth I] 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		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain HA [auth H] SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain TA [auth L] SDF format, chain S [auth C] SDF format, chain QA [auth K] SDF format, chain P [auth B] SDF format, chain NA [auth J] SDF format, chain M [auth A] SDF format, chain KA [auth I] SDF format, chain EA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain HA [auth H] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain TA [auth L] MOL2 format, chain S [auth C] MOL2 format, chain QA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain EA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain HA [auth H] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain TA [auth L] mmCIF format, chain S [auth C] mmCIF format, chain QA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain EA [auth G]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] 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		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain UA [auth L] SDF format, chain T [auth C] SDF format, chain RA [auth K] SDF format, chain Q [auth B] SDF format, chain OA [auth J] SDF format, chain N [auth A] SDF format, chain LA [auth I] SDF format, chain IA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain UA [auth L] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth K] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain UA [auth L] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth K] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] IA [auth H] LA [auth I] N [auth A] 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		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain T [auth C] Focus chain UA [auth L] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain T [auth C] Focus chain UA [auth L] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.224 (Depositor), 0.225 (DCC)
R-Value Work: 0.215 (Depositor), 0.217 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.778	α = 90
b = 133.225	β = 93.99
c = 95.228	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-10-09

Deposition Author(s):

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
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description