New Insights into Thermostability of Bacterial Ferredoxins: High Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus thermophilus

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

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This is version 1.3 of the entry. See complete history


New Insights Into the Thermostability of Bacterial Ferredoxins: High-Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus Thermophilus

Macedo-Ribeiro, S.Martins, B.M.Pereira, P.J.B.Buse, G.Huber, R.Soulimane, T.

(2001) J Biol Inorg Chem 6: 663

  • DOI: https://doi.org/10.1007/s007750100243
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the seven-iron ferredoxin from Thermus thermophilus (FdTt) has been determined at 1.64 A resolution, allowing us to unveil the common mechanisms of thermostabilization within "bacterial-type" ferredoxins. FdTt and other homologous thermophilic seven-iron ferredoxins are smaller than their mesophilic counterparts. Thermostabilizing features are optimized in a minimal structural and functional unit, with an extensive cross-linking of secondary structure elements mediated by improved polar and hydrophobic interactions. Most of the potentially stabilizing features are focused on the vicinity of the functional [3Fe-4S] cluster. The structural [4Fe-4S] cluster is shielded in thermophilic FdTt by an increased number of polar interactions involving the two N-terminal residues. Comparisons with the hyperthermostable ferredoxin from Thermotoga maritima reveal that (1) a reduction in the number of non-glycine residues in strained conformations, (2) improved polar interactions within the common iron-sulfur cluster binding (betaalphabeta)2 motif, and (3) an optimized charge distribution at the protein surface, constitute a common strategy for increasing the thermal stability of these ferredoxins.

  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschungm, Martinsried, Germany. sandra@aramis.ibmc.up.pt

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERREDOXIN78Thermus aquaticusMutation(s): 0 
Find proteins for P03942 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P03942 
Go to UniProtKB:  P03942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03942
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SF4

Download Ideal Coordinates CCD File 
Fe4 S4
Query on F3S

Download Ideal Coordinates CCD File 
C [auth A]FE3-S4 CLUSTER
Fe3 S4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.7α = 90
b = 42.12β = 90
c = 62.99γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-27
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description