1iqz
From Proteopedia
(New page: 200px<br /><applet load="1iqz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1iqz, resolution 0.92Å" /> '''OXIDIZED [4Fe-4S] FE...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1iqz.jpg|left|200px]]<br /><applet load="1iqz" size=" | + | [[Image:1iqz.jpg|left|200px]]<br /><applet load="1iqz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1iqz, resolution 0.92Å" /> | caption="1iqz, resolution 0.92Å" /> | ||
'''OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM I)'''<br /> | '''OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM I)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] | + | Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 A and 1.00 A 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 A resolution data of the form I and 11.2 % for the 13.3-1.0 A 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 A resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C(alpha)-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. |
==About this Structure== | ==About this Structure== | ||
| - | 1IQZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus] with SO4 and SF4 as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 1IQZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=SF4:'>SF4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entries 2FXB and 1FXB. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQZ OCA]. |
==Reference== | ==Reference== | ||
| Line 24: | Line 24: | ||
[[Category: ultlahigh resolution analysis]] | [[Category: ultlahigh resolution analysis]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:14:40 2008'' |
Revision as of 11:14, 21 February 2008
|
OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM I)
Overview
Diffraction data of two crystal forms (forms I and II) of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus have been collected to 0.92 A and 1.00 A 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 A resolution data of the form I and 11.2 % for the 13.3-1.0 A 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 A resolution; the largest correction was that the main-chain of Pro1 and the side-chain of Lys2 were changed by rotating the C(alpha)-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.
About this Structure
1IQZ is a Single protein structure of sequence from Bacillus thermoproteolyticus with and as ligands. This structure supersedes the now removed PDB entries 2FXB and 1FXB. Full crystallographic information is available from OCA.
Reference
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 K, Okada T, Kakuta Y, Takahashi Y, J Mol Biol. 2002 Feb 1;315(5):1155-66. PMID:11827483[[Category: geometry of [4fe-4s] cluster]]
Page seeded by OCA on Thu Feb 21 13:14:40 2008
