Abstract
Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 Å and 1.00 Å resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8% for 7.0-0.92 Å resolution data of the form I and 11.2% for the 13.3-1.0 Å resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 Å resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C α -C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D 2d symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.
| Original language | English |
|---|---|
| Pages (from-to) | 1155-1166 |
| Number of pages | 12 |
| Journal | Journal of Molecular Biology |
| Volume | 315 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - Jan 1 2002 |
| Externally published | Yes |
Fingerprint
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology
Cite this
Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms : Systematic distortion of [4Fe-4S] cluster in the protein. / Fukuyama, Keiichi; Okada, Toshihiro; Kakuta, Yoshimitsu; Takahashi, Yasuhiro.
In: Journal of Molecular Biology, Vol. 315, No. 5, 01.01.2002, p. 1155-1166.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms
T2 - Systematic distortion of [4Fe-4S] cluster in the protein
AU - Fukuyama, Keiichi
AU - Okada, Toshihiro
AU - Kakuta, Yoshimitsu
AU - Takahashi, Yasuhiro
PY - 2002/1/1
Y1 - 2002/1/1
N2 - Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 Å and 1.00 Å resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8% for 7.0-0.92 Å resolution data of the form I and 11.2% for the 13.3-1.0 Å resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 Å resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C α -C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D 2d symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.
AB - Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 Å and 1.00 Å resolutions, respectively, at 100 K using synchrotron radiation. Anisotropic temperature factors were introduced for all non-hydrogen atoms in the refinement with SHELX-97, in which stereochemical restraints were applied to the protein chain but not to the [4Fe-4S] cluster. The final crystallographic R-factors are 9.8% for 7.0-0.92 Å resolution data of the form I and 11.2% for the 13.3-1.0 Å resolution data of the form II. Many hydrogen atoms as well as multiple conformations for several side-chains have been identified. The present refinement has revised the conformations of several peptide bonds and side-chains assigned previously at 2.3 Å resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C α -C bond of Lys2. Although the overall structures in the two crystal forms are very similar, conformational differences are observed in the two residues at the middle (Glu29 and Asp30) and the C-terminal residues, which have large temperature factors. The [4Fe-4S] cluster is a distorted cube with non-planar rhombic faces. Slight but significant compression of the four Fe-S bonds along one direction is observed in both crystal forms, and results in the D 2d symmetry of the cluster. The compressed direction of the cluster relative to the protein is conserved in the two crystal forms and consistent with that in one of the clusters in Clostridium acidurici ferredoxin.
UR - http://www.scopus.com/inward/record.url?scp=0036301033&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036301033&partnerID=8YFLogxK
U2 - 10.1006/jmbi.2001.5292
DO - 10.1006/jmbi.2001.5292
M3 - Article
VL - 315
SP - 1155
EP - 1166
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 5
ER -