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
N1 - Funding Information:
We thank Dr Kazuhiko Saeki for providing us with the synthetic oligonucleotides for the BtFd gene, Drs Masahide Kawamoto and Keiko Miura of SPring-8 for their valuable help with the data collection using synchrotron radiation, and Professor Norikazu Ueyama for his valuable suggestions. A part of this research was done with the approval of the SPring-8 Proposal Review Committee (proposals no. 2000A0489-UL and 2000B0341-NL). We also thank the staff of the Research Center for Structural Biology, Institute for Protein Research, for use of the four-circle diffractometer. This work was supported in part by a Grant-in-Aid for Scientific Research on a Priority Area (Biological Machinery no. 11169223) from the Ministry of Education, Culture, Sports, Science and Technology of Japan to K.F. and by the Sakabe Project of TARA (Tsukuba Advanced Research Alliance) of the University of Tsukuba.
PY - 2002
Y1 - 2002
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 Cα-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 D2d 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 Cα-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 D2d 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.
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U2 - 10.1006/jmbi.2001.5292
DO - 10.1006/jmbi.2001.5292
M3 - Article
C2 - 11827483
AN - SCOPUS:0036301033
VL - 315
SP - 1155
EP - 1166
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 5
ER -