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PDBsum entry 2fdn
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Electron transport PDB id
2fdn

 

 

 

 

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Contents
Protein chain
55 a.a. *
Ligands
SF4 ×2
Waters ×94
* Residue conservation analysis
PDB id:
2fdn
Name: Electron transport
Title: 2[4fe-4s] ferredoxin from clostridium acidi-urici
Structure: Ferredoxin. Chain: a
Source: Clostridium acidurici. Organism_taxid: 1556. Atcc: 7906
Resolution:
0.94Å     R-factor:   0.100    
Authors: Z.Dauter,K.S.Wilson,L.C.Sieker,J.Meyer,J.M.Moulis
Key ref:
Z.Dauter et al. (1997). Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein. Biochemistry, 36, 16065-16073. PubMed id: 9405040 DOI: 10.1021/bi972155y
Date:
01-Oct-97     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00198  (FER_CLOA9) -  4Fe-4S ferredoxin FdxA from Gottschalkia acidurici (strain ATCC 7906 / DSM 604 / BCRC 14475 / CIP 104303 / KCTC 5404 / NCIMB 10678 / 9a)
Seq:
Struc: 		56 a.a.
55 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi972155y Biochemistry 36:16065-16073 (1997)
PubMed id: 9405040  
 
 
Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein.
Z.Dauter, K.S.Wilson, L.C.Sieker, J.Meyer, J.M.Moulis.
 
  ABSTRACT  
 
The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been solved using X-ray diffraction data extending to atomic resolution, 0.94 A, recorded at 100 K. The model was refined with anisotropic representation of atomic displacement parameters for all non-hydrogen atoms and with hydrogens riding on their parent atoms. Stereochemical restraints were applied to the protein chain but not to the iron-sulfur clusters. The final R factor is 10.03 % for all data. Inversion of the final least-squares matrix allowed direct estimation of the errors of individual parameters. The estimated errors in positions for protein main chain atoms are below 0.02 A and about 0.003 A for the heavier [4Fe-4S] cluster atoms. Significant differences between the stereochemistry of the two clusters and distortion of both of them from ideal Td tetrahedral symmetry can be defined in detail at this level of accuracy. Regions of alternative conformations include not only protein side chains but also two regions of the main chain. One such region is the loop of residues 25-29, which was highly disordered in the room temperature structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
20635418 B.S.Perrin, and T.Ichiye (2010).
Fold versus sequence effects on the driving force for protein-mediated electron transfer.
  Proteins, 78, 2798-2808.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
19290553 E.Saridakis, P.Giastas, G.Efthymiou, V.Thoma, J.M.Moulis, P.Kyritsis, and I.M.Mavridis (2009).
Insight into the protein and solvent contributions to the reduction potentials of [4Fe-4S]2+/+ clusters: crystal structures of the Allochromatium vinosum ferredoxin variants C57A and V13G and the homologous Escherichia coli ferredoxin.
  J Biol Inorg Chem, 14, 783-799.
PDB codes: 2zvs 3eun 3exy
19380375 M.Sokolowska, H.Czapinska, and M.Bochtler (2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
  Nucleic Acids Res, 37, 3799-3810.
PDB codes: 3fc3 3gox
17992543 J.Meyer (2008).
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution.
  J Biol Inorg Chem, 13, 157-170.  
18400755 Y.Nicolet, J.K.Rubach, M.C.Posewitz, P.Amara, C.Mathevon, M.Atta, M.Fontecave, and J.C.Fontecilla-Camps (2008).
X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima.
  J Biol Chem, 283, 18861-18872.
PDB codes: 3ciw 3cix
17292835 D.A.Kondrashov, A.W.Van Wynsberghe, R.M.Bannen, Q.Cui, and G.N.Phillips (2007).
Protein structural variation in computational models and crystallographic data.
  Structure, 15, 169-177.  
17457690 M.Heinnickel, and J.H.Golbeck (2007).
Heliobacterial photosynthesis.
  Photosynth Res, 92, 35-53.  
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
16596388 P.Giastas, N.Pinotsis, G.Efthymiou, M.Wilmanns, P.Kyritsis, J.M.Moulis, and I.M.Mavridis (2006).
The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values.
  J Biol Inorg Chem, 11, 445-458.
PDB code: 2fgo
16673033 Y.Xiao, M.Koutmos, D.A.Case, D.Coucouvanis, H.Wang, and S.P.Cramer (2006).
Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.
  Dalton Trans, (), 2192-2201.  
16301796 P.Skubák, S.Ness, and N.S.Pannu (2005).
Extending the resolution and phase-quality limits in automated model building with iterative refinement.
  Acta Crystallogr D Biol Crystallogr, 61, 1626-1635.  
12089152 A.P.Yeh, X.I.Ambroggio, S.L.Andrade, O.Einsle, C.Chatelet, J.Meyer, and D.C.Rees (2002).
High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.
  J Biol Chem, 277, 34499-34507.
PDB codes: 1m2a 1m2b 1m2d
11842205 G.Fritz, A.Roth, A.Schiffer, T.Büchert, G.Bourenkov, H.D.Bartunik, H.Huber, K.O.Stetter, P.M.Kroneck, and U.Ermler (2002).
Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution.
  Proc Natl Acad Sci U S A, 99, 1836-1841.
PDB codes: 1jnr 1jnz
12455953 J.E.Nixon, A.Wang, J.Field, H.G.Morrison, A.G.McArthur, M.L.Sogin, B.J.Loftus, and J.Samuelson (2002).
Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica.
  Eukaryot Cell, 1, 181-190.  
12077433 J.Symersky, Y.Devedjiev, K.Moore, C.Brouillette, and L.DeLucas (2002).
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 1138-1146.
PDB code: 1kqp
11704670 K.Chen, Y.S.Jung, C.A.Bonagura, G.J.Tilley, G.S.Prasad, V.Sridhar, F.A.Armstrong, C.D.Stout, and B.K.Burgess (2002).
Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential.
  J Biol Chem, 277, 5603-5610.
PDB codes: 1g3o 1g6b 1gao
12198302 M.L.Baniecki, W.J.McGrath, Z.Dauter, and W.F.Mangel (2002).
Adenovirus proteinase: crystallization and preliminary X-ray diffraction studies to atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 58, 1462-1464.  
11812787 X.Brazzolotto, P.Timmins, Y.Dupont, and J.M.Moulis (2002).
Structural changes associated with switching activities of human iron regulatory protein 1.
  J Biol Chem, 277, 11995-12000.  
11856836 Z.Dauter, M.Dauter, and E.Dodson (2002).
Jolly SAD.
  Acta Crystallogr D Biol Crystallogr, 58, 494-506.  
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.  
11568186 K.S.Yoon, C.Bobst, C.F.Hemann, R.Hille, and F.R.Tabita (2001).
Spectroscopic and functional properties of novel 2[4Fe-4S] cluster-containing ferredoxins from the green sulfur bacterium Chlorobium tepidum.
  J Biol Chem, 276, 44027-44036.  
11524134 P.M.Vignais, B.Billoud, and J.Meyer (2001).
Classification and phylogeny of hydrogenases.
  FEMS Microbiol Rev, 25, 455-501.  
11264580 R.A.Steiner, H.J.Rozeboom, A.de Vries, K.H.Kalk, G.N.Murshudov, K.S.Wilson, and B.W.Dijkstra (2001).
X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 516-526.
PDB code: 1g4i
10666594 D.Housset, F.Benabicha, V.Pichon-Pesme, C.Jelsch, A.Maierhofer, S.David, J.C.Fontecilla-Camps, and C.Lecomte (2000).
Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 A resolution as a first test case.
  Acta Crystallogr D Biol Crystallogr, 56, 151-160.  
10387068 C.G.Schipke, D.B.Goodin, D.E.McRee, and C.D.Stout (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.
PDB codes: 6fdr 7fd1 7fdr
10329772 E.A.Merritt (1999).
Expanding the model: anisotropic displacement parameters in protein structure refinement.
  Acta Crystallogr D Biol Crystallogr, 55, 1109-1117.  
10531472 E.Parisini, F.Capozzi, P.Lubini, V.Lamzin, C.Luchinat, and G.M.Sheldrick (1999).
Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 1773-1784.
PDB codes: 1b0y 1cku
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
10607667 M.H.Charon, A.Volbeda, E.Chabriere, L.Pieulle, and J.C.Fontecilla-Camps (1999).
Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase.
  Curr Opin Struct Biol, 9, 663-669.  
10545324 M.T.Bes, E.Parisini, L.A.Inda, L.M.Saraiva, M.L.Peleato, and G.M.Sheldrick (1999).
Crystal structure determination at 1.4 A resolution of ferredoxin from the green alga Chlorella fusca.
  Structure, 7, 1201-1211.
PDB code: 1awd
10320364 P.Kyritsis, R.Kümmerle, J.G.Huber, J.Gaillard, B.Guigliarelli, C.Popescu, E.Münck, and J.M.Moulis (1999).
Unusual NMR, EPR, and Mössbauer properties of Chromatium vinosum 2[4Fe-4S] ferredoxin.
  Biochemistry, 38, 6335-6345.  
9624123 P.Kyritsis, O.M.Hatzfeld, T.A.Link, and J.M.Moulis (1998).
The two [4Fe-4S] clusters in Chromatium vinosum ferredoxin have largely different reduction potentials. Structural origin and functional consequences.
  J Biol Chem, 273, 15404-15411.  
9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
  Curr Opin Struct Biol, 8, 730-737.  
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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