1JGC

The 2.6 A Structure Resolution of Rhodobacter capsulatus Bacterioferritin with Metal-free Dinuclear Site and Heme Iron in a Crystallographic Special Position

Summary for 1JGC

• Entry DOI: 10.2210/pdb1jgc/pdb
• Descriptor: bacterioferritin, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: iron storage protein, metal binding protein
• Biological source: Rhodobacter capsulatus
• Total number of polymer chains: 3
• Total formula weight: 56436.24

Authors

Cobessi, D.,Huang, L.-S.,Ban, M.,Pon, N.G.,Daldal, F.,Berry, E.A. (deposition date: 2001-06-24, release date: 2002-01-09, Last modification date: 2024-12-25)

Primary citation

Cobessi, D.,Huang, L.S.,Ban, M.,Pon, N.G.,Daldal, F.,Berry, E.A.
The 2.6 A resolution structure of Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a crystallographic 'special position'.
Acta Crystallogr.,Sect.D, 58:29-38, 2002

PubMed Abstract: Bacterioferritin from Rhodobacter capsulatus was crystallized and its structure was solved at 2.6 A resolution. This first structure of a bacterioferritin from a photosynthetic organism is a spherical particle of 24 subunits displaying 432 point-group symmetry like ferritin and bacterioferritin from Escherichia coli. Crystallized in the I422 space group, its structural analysis reveals for the first time the non-symmetric heme molecule located on a twofold crystallographic symmetry axis. Other hemes of the protomer are situated on twofold noncrystallographic axes. Apparently, both types of sites bind heme in two orientations, leading to an average structure consisting of a symmetric 50:50 mixture, thus satisfying the crystallographic and noncrystallographic symmetry of the crystal. Five water molecules are situated close to the heme, which is bound in a hydrophobic pocket and axially coordinated by two crystallographic or noncrystallographically related methionine residues. Its ferroxidase center, in which Fe(II) is oxidized to Fe(III), is empty or fractionally occupied by a metal ion. Two positions are observed for the coordinating Glu18 side chain instead of one in the E. coli enzyme in which the site is occupied. This result suggests that the orientation of the Glu18 side chain could be constrained by this interaction.

PubMed: 11752777
DOI: 10.1107/S0907444901017267

Experimental method

X-RAY DIFFRACTION (2.6 Å)