PDBsum entry 6fd1

Electron transport

PDB id: 6fd1

Contents

Protein chain

106 a.a.

Ligands

SF4

F3S

Waters ×162

References listed in PDB file

Key reference

Title

Structure of azotobacter vinelandii 7fe ferredoxin at 1.35 a resolution and determination of the [fe-S] bonds with 0.01 a accuracy.

Authors

C.D.Stout, E.A.Stura, D.E.Mcree.

Ref.

J Mol Biol, 1998, 278, 629-639. [DOI no: 10.1006/jmbi.1998.1732]

PubMed id

9600844

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 92%.

Abstract

The crystal structure of Azotobacter vinelandii ferredoxin I (FdI) at 100 K has been refined at 1.35 A resolution by full matrix block diagonal least-squares methods with anisotropic temperature factors for all non-hydrogen atoms and with hydrogen atoms included in the model. Fe-S bonds within the [3Fe-4S]+ and [4Fe-4S]2+ clusters of the protein are determined with an accuracy of at least 0.01 A. Analysis of metric parameters reveals greater variation in bonds and angles within the [3Fe-4S]+ cluster than in the [4Fe-4S]2+ cluster, whereas the opposite is true regarding the cysteine Sgamma atoms ligating to the two [Fe-S] cores. The [3Fe-4S]+ core is asymmetrically distorted by the protein matrix but relatively uniformly ligated by its three Cys ligands; in contrast the tetrahedral [4Fe-4S]2+ core is relatively symmetric but non-uniformily ligated by its four Cys ligands, three of which occur in a conserved CysxxCysxxCys residue motif. Comparison of the [3Fe-4S]+ clusters in FdI and Desulfovibrio gigas ferredoxin II, refined at 1.7 A resolution, indicates that within the limit of accuracy of the two refinements the cuboidal core is differently distorted in the two proteins. Comparison of the [3Fe-4S]+ core in FdI with the structure of a reduced [Fe3S4]o synthetic analog indicates that the protein-bound cluster displays distortions not intrinsic to the core itself. Nevertheless, both [3Fe-4S]+ and [Fe3S4]o cores have metric features consistent with expected trends due to net charge on Fe and valency of S, and both exhibit a splayed configuration with respect to their three mu2S atoms in the absence of a fourth Fe. Comparison of the [4Fe-4S]2+ cluster in FdI with the structures of [Fe4S4]2+ synthetic analogs shows that the protein bound and synthetic cubanes are very similar in geometric parameters, including the presence of tetragonal distortion in the FdI cluster common to this oxidation state.

Figure 1.
Figure 1. Electron density for the [3Fe-4S]+ (a) and [4Fe-4S]2+ (b) clusters and the Sg atoms of their Cys ligands in FdI at 1.35 Å resolution. Coordinates are from the final cycle of refinement and the map is calculated with all the data, coeficients 2|F[o]| - |F[c]| and sA weights, and contoured at 5s.

Figure 2.
Figure 2. Thermal ellipsoids for the Fe and S atoms of the [3Fe-4S]^+ (a) and [4Fe-4S]^2+ (b) clusters and their S^γ ligand atoms. Coordinates and U[ij] parameters are from the final cycle of refinement. The major axes of the ellipses are plotted at 50% probability, and the volumes depicted represent the 25% probability ellipsoids. The orientation of each cluster is the same as in Figure 1. Note that the shapes of the ellipsoids manifest the asymmetry of the observed electron density.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 629-639) copyright 1998.