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 1.2 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


  • 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 doubl ...

    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: 
    • 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
    • Structure of Synechococcus Elongatus [Fe2S2] Ferredoxin in Solution
      Baumann, B.,Sticht, H.,Scharpf, M.,Sutter, M.,Haehnel, W.,Rosch, P.
      (1996) Biochemistry 35: 12831
    • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
96Petroselinum crispum
Find proteins for Q7M1S1 (Petroselinum crispum)
Go to UniProtKB:  Q7M1S1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
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 
  • Olderado: 1PFD Olderado
Software Package:
Software NamePurpose
DYANArefinement
AMBERrefinement
DYANAmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance