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PDBsum entry 7fdr    Go to PDB code:               Electron transport PDB id 7fdr    Loading ...       Contents  Protein chain  106 a.a.* Ligands SF4 F3S Waters ×142 * Residue conservation analysis PDB id: 7fdr  Links PDBe RCSB MMDB JenaLib Proteopedia CATH SCOP PDBSWS PDBePISA CSA ProSAT Name: Electron transport Title: 7-fe ferredoxin from azotobacter vinelandii, na dithionite reduced, ph 8.5, 1.4a resolution, 100 k Structure: Protein (7-fe ferredoxin i). Chain: a. Synonym: fd1 Source: Azotobacter vinelandii. Organism_taxid: 354 Resolution: 1.40Å R-factor: 0.170 Authors: C.G.Schipke,D.B.Goodin,D.E.Mcree,C.D.Stout Key ref:  C.G.Schipke et al. (1999). Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.Biochemistry,38, 8228-8239.PubMed id: 10387068 DOI: 10.1021/bi983008i Date: 11-Dec-98 Release date: 16-Dec-98 PROCHECK   Headers  References   Protein chain        ?  P00214 (FER1_AZOVI) - Ferredoxin-1 from Azotobacter vinelandii Seq:Struc: 107 a.a. 106 a.a.   Key:  PfamA domain  Secondary structure  CATH domain  DOI no: 10.1021/bi983008i Biochemistry 38:8228-8239 (1999) PubMed id: 10387068 Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster. C.G.Schipke, D.B.Goodin, D.E.McRee, C.D.Stout. ABSTRACT The refined structure of reduced Azotobacter vinelandii 7Fe ferredoxin FdI at 100 K and 1.4 A resolution is reported, permitting comparison of [3Fe-4S]+ and [3Fe-4S]0 clusters in the same protein at near atomic resolution. The reduced state of the [3Fe-4S]0 cluster is established by single-crystal EPR following data collection. Redundant structures are refined to establish the reproducibility and accuracy of the results for both oxidation states. The structure of the [4Fe-4S]2+ cluster in four independently determined FdI structures is the same within the range of derived standard uncertainties, providing an internal control on the experimental methods and the refinement results. The structures of the [3Fe-4S]+ and [3Fe-4S]0 clusters are also the same within experimental error, indicating that the protein may be enforcing an entatic state upon this cluster, facilitating electron-transfer reactions. The structure of the FdI [3Fe-4S]0 cluster allows direct comparison with the structure of a well-characterized [Fe3S4]0 synthetic analogue compound. The [3Fe-4S]0 cluster displays significant distortions with respect to the [Fe3S4]0 analogue, further suggesting that the observed [3Fe-4S]+/0 geometry in FdI may represent an entatic state. Comparison of oxidized and reduced FdI reveals conformational changes at the protein surface in response to reduction of the [3Fe-4S]+/0 cluster. The carboxyl group of Asp15 rotates approximately 90 degrees, Lys84, a residue hydrogen bonded to Asp15, adopts a single conformation, and additional H2O molecules become ordered. These structural changes imply a mechanism for H+ transfer to the [3Fe-4S]0 cluster in agreement with electrochemical and spectroscopic results.    Literature references that cite this PDB file's key reference PubMed id Reference 18072179 S.Lammers, S.Lutz, and M.Meuwly (2008). Reactive force fields for proton transfer dynamics. J Comput Chem,29, 1048-1063. 15041642 M.Meuwly, and M.Karplus (2004). Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron transfer on protein dynamics. Biophys J,86, 1987-2007. 12750363 I.Bento, V.H.Teixeira, A.M.Baptista, C.M.Soares, P.M.Matias, and M.A.Carrondo (2003). Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J Biol Chem,278, 36455-36469. PDB codes: 1ofw 1ofy 11463610 B.W.Beck, Q.Xie, and T.Ichiye (2001). Sequence determination of reduction potentials by cysteinyl hydrogen bonds and peptide pipoles in [4Fe-4S] ferredoxins. Biophys J,81, 601-613. 11334783 D.A.Cherepanov, and A.Y.Mulkidjanian (2001). Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15. Biochim Biophys Acta,1505, 179-184. 11344329 T.Min, C.E.Ergenekan, M.K.Eidsness, T.Ichiye, and C.Kang (2001). Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin. Protein Sci,10, 613-621. PDB codes: 1fhh 1fhm 10593945 K.Chen, G.J.Tilley, V.Sridhar, G.S.Prasad, C.D.Stout, F.A.Armstrong, and B.K.Burgess (1999). Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I. J Biol Chem,274, 36479-36487. PDB code: 1b0v The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right. |
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