3BVK | pdb_00003bvk

Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin

PDB DOI: https://doi.org/10.2210/pdb3BVK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-07 Released: 2009-01-13
Deposition Author(s): Kim, K.H., Cho, K.J., Lee, J.H., Shin, H.J., Yang, I.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.194 (Depositor), 0.193 (DCC)
R-Value Work:
0.174 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin

Kim, K.H., Cho, K.J., Lee, J.H., Shin, H.J., Yang, I.S.

To be published.

Macromolecule Content

Total Structure Weight: 126.8 kDa
Atom Count: 9,915
Modeled Residue Count: 1,032
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E A, B, C, D, E, F	181	Helicobacter pylori	Mutation(s): 0 EC: 1.16.3.1 (PDB Primary Data), 1.16.3.2 (UniProt)
UniProt
Find proteins for Q9ZLI1 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZLI1 Go to UniProtKB: Q9ZLI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ZLI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain W [auth F] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain W [auth F] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain W [auth F]	L [auth B], O [auth C], W [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain O [auth C] Focus chain W [auth F] Interactions & Density Focus chain L [auth B] Focus chain O [auth C] Focus chain W [auth F]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth E], U [auth F], V [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.194 (Depositor), 0.193 (DCC)
R-Value Work: 0.174 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.454	α = 90
b = 128.454	β = 90
c = 165.334	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-01-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references