1PFD

THE SOLUTION STRUCTURE OF HIGH PLANT PARSLEY [2FE-2S] FERREDOXIN, NMR, 18 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 18 
  • Selection Criteria: LEAST TARGET FUNCTION 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The solution structure of parsley [2Fe-2S]ferredoxin.

Im, S.C.Liu, G.Luchinat, C.Sykes, A.G.Bertini, I.

(1998) Eur J Biochem 258: 465-477

  • DOI: 10.1046/j.1432-1327.1998.2580465.x
  • Primary Citation of Related Structures:  
    1PFD

  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Structure of Synechococcus Elongatus [Fe2S2] Ferredoxin in Solution
      Baumann, B., Sticht, H., Scharpf, M., Sutter, M., Haehnel, W., Rosch, P.
      (1996) Biochemistry 35: 12831
    • 1H and 15N NMR Sequential Assignment, Secondary Structure, and Tertiary Fold of [2Fe-2S] Ferredoxin from Synechocystis Sp. Pcc 6803
      Lelong, C., Setif, P., Bottin, H., Andre, F., Neumann, J.M.
      (1995) Biochemistry 34: 14462
    • An NMR-Derived Model for the Solution Structure of Oxidized Putidaredoxin, a 2-Fe, 2-S Ferredoxin from Pseudomonas
      Pochapsky, T.C., Ye, X.M., Ratnaswamy, G., Lyons, T.A.
      (1994) Biochemistry 33: 6424
    • Multinuclear Magnetic Resonance Studies of the 2Fe(Dot)2Sferredoxin from Anabaena Species Strain Pcc 7120. 1. Sequence-Specific Hydrogen-1 Resonance Assignments and Secondary Structure in Solution of the Oxidized Form
      Oh, B.H., Markley, J.L.
      (1990) Biochemistry 29: 3993

    Organizational Affiliation

    Department of Chemistry, University of Florence, Italy.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERREDOXINA96Petroselinum crispumMutation(s): 0 
EC: 1.7.7.2
UniProt
Find proteins for Q7M1S1 (Petroselinum crispum)
Explore Q7M1S1 
Go to UniProtKB:  Q7M1S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M1S1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 18 
  • Selection Criteria: LEAST TARGET FUNCTION 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations, Other