PDBsum entry 1pfd

Go to PDB code: 
protein ligands links
Electron transport PDB id
Protein chain
96 a.a. *
* Residue conservation analysis
PDB id:
Name: Electron transport
Title: The solution structure of high plant parsley [2fe-2s] ferredoxin, nmr, 18 structures
Structure: Ferredoxin. Chain: a. Ec:
Source: Petroselinum crispum. Parsley. Organism_taxid: 4043. Organ: leaves
NMR struc: 18 models
Authors: S.-C.Im,G.Liu,C.Luchinat,A.G.Sykes,I.Bertini
Key ref:
S.C.Im et al. (1998). The solution structure of parsley [2Fe-2S]ferredoxin. Eur J Biochem, 258, 465-477. PubMed id: 9874213 DOI: 10.1046/j.1432-1327.1998.2580465.x
05-May-98     Release date:   11-May-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q7M1S1  (Q7M1S1_PETCR) -  Ferredoxin
96 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     electron transport chain   1 term 
  Biochemical function     electron carrier activity     4 terms  


DOI no: 10.1046/j.1432-1327.1998.2580465.x Eur J Biochem 258:465-477 (1998)
PubMed id: 9874213  
The solution structure of parsley [2Fe-2S]ferredoxin.
S.C.Im, G.Liu, C.Luchinat, A.G.Sykes, I.Bertini.
The [2Fe-2S]ferredoxin I (Fd I) from parsley leaves (Mr = 10,500; 96 amino acids) in the Fe(III)-Fe(III) oxidized form has been studied by 1H-NMR spectroscopy. Sequence-specific 1H-NMR assignments were obtained through two-dimensional classical double-quantum-filtered-COSY, NOESY and TOCSY spectra. NOEs between protons as close as 5.6 A from the paramagnetic Fe(III) atoms were observed at 800 MHz. A total of 3066 NOEs (of which 2533 are meaningful) and 18 distance constraints taken from X-ray crystallography of the Fe2S2 active site were used to obtain the solution structure. From inversion recovery NOESY experiments, 33 longitudinal relaxation rate (Qpara) constraints were used for the structural refinement. The final structure was obtained by a process of restrained energy minimization. Root-mean-square (rmsd) deviation values obtained for the family of 18 structures (with reference to the average structure) are 0.52 +/- 0.10 A and 0.91 +/- 0.12 A for backbone and all heavy atoms respectively. The structure consists of seven-strands of beta-sheets and four short alpha-helices. The quality of the present solution structure is among the best of those reported for [2Fe-2S]ferredoxins. The secondary structure and overall folding are compared with those of Anabaena variabilis Fd and the higher plant Equistum arvense (horse tail) protein determined through X-ray crystallography. The groups believed to be responsible for electron transfer have been analysed.
  Selected figure(s)  
Figure 2.
Fig. 2. Schematic representation of sequential connectivities involving HN, HB and H# protons of parsley ferredoxin I. For the sequential connectivities, the thickness of the bar indicates the NOE intensity. The medium­range NOEs are identified by lines connecting the two correlated residues.
Figure 6.
Fig. 6. Comparison of the solution structure of parsley Fd I with the X­ray structures of two [2Fe­2S]ferredoxins: (a) parsley ferredoxin I; (b) E. arvense ferredoxin [16]; (c) A. variabilis PCC7120 ferredoxin [13, 14].
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (1998, 258, 465-477) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16731971 M.Nouailler, X.Morelli, O.Bornet, B.Chetrit, Z.Dermoun, and F.Guerlesquin (2006).
Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex.
  Protein Sci, 15, 1369-1378.
PDB code: 2auv
11746708 I.Bertini, C.Luchinat, A.Provenzani, A.Rosato, and P.R.Vasos (2002).
Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.
  Proteins, 46, 110-127.  
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 code is shown on the right.