2VKR | pdb_00002vkr

3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.273 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

Frazao, C., Aragao, D., Coelho, R., Leal, S.S., Gomes, C.M., Teixeira, M., Carrondo, M.A.

(2008) FEBS Lett 582: 763-767

  • DOI: https://doi.org/10.1016/j.febslet.2008.01.041
  • Primary Citation of Related Structures:  
    2VKR

  • PubMed Abstract: 

    Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II.

    • Organizational Affiliation: 

    Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av da República, Oeiras, Portugal. frazao@itqb.unl.pt


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ZINC-CONTAINING FERREDOXIN
A, B, C, D, E
103Acidianus ambivalensMutation(s): 0 
UniProt
Find proteins for P49949 (Acidianus ambivalens)
Explore P49949 
Go to UniProtKB:  P49949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49949
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
AA [auth G]
I [auth A]
L [auth B]
O [auth C]
R [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S
Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth G]
J [auth A]
M [auth B]
P [auth C]
S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.273 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.5α = 90
b = 117.5β = 90
c = 50.9γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-03-29
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 1.6: 2024-02-07
    Changes: Data collection, Refinement description