1NF6

X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans

Macedo, S.Romao, C.V.Mitchell, E.Matias, P.M.Liu, M.Y.Xavier, A.V.LeGall, J.Teixeira, M.Lindley, P.Carrondo, M.A.

(2003) Nat Struct Biol 10: 285-290

  • DOI: 10.1038/nsb909
  • Primary Citation of Related Structures:  
    1NF6, 1NF4, 1NFV

  • PubMed Abstract: 
  • The first crystal structure of a native di-iron center in an iron-storage protein (bacterio)ferritin is reported. The protein, isolated from the anaerobic bacterium Desulfovibrio desulfuricans, has the unique property of having Fe-coproporphyrin III as its heme cofactor ...

    The first crystal structure of a native di-iron center in an iron-storage protein (bacterio)ferritin is reported. The protein, isolated from the anaerobic bacterium Desulfovibrio desulfuricans, has the unique property of having Fe-coproporphyrin III as its heme cofactor. The three-dimensional structure of this bacterioferritin was determined in three distinct catalytic/redox states by X-ray crystallography (at 1.95, 2.05 and 2.35 A resolution), corresponding to different intermediates of the di-iron ferroxidase site. Conformational changes associated with these intermediates support the idea of a route for iron entry into the protein shell through a pore that passes through the di-iron center. Molecular surface and electrostatic potential calculations also suggest the presence of another ion channel, distant from the channels at the three- and four-fold axes proposed as points of entry for the iron atoms.


    Related Citations: 
    • Structure determination of bacterioferritin from Desulfovibrio desulfuricans by the MAD method at the Fe K-edge
      Coelho, A.V., Macedo, S., Matias, P.M., Thompson, A.W., LeGall, J., Carrondo, M.A.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 326

    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, EAN, Apartado 127, 2781-901 Oeiras, Portugal.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
bacterioferritin
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
179Desulfovibrio desulfuricansMutation(s): 0 
EC: 1.16.3.1
Find proteins for Q93PP9 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore Q93PP9 
Go to UniProtKB:  Q93PP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEC
Query on FEC

Download Ideal Coordinates CCD File 
AA [auth C], EB [auth K], JA [auth F], NA [auth G], QB [auth N], TB [auth O], U [auth A], VA [auth I]1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BB [auth K] , CA [auth D] , CB [auth K] , DA [auth E] , DB [auth K] , FA [auth E] , GB [auth L] , HA [auth F] , 
BB [auth K],  CA [auth D],  CB [auth K],  DA [auth E],  DB [auth K],  FA [auth E],  GB [auth L],  HA [auth F],  HB [auth L],  IA [auth F],  JB [auth M],  KB [auth M],  LA [auth G],  LB [auth M],  MA [auth G],  MB [auth N],  OB [auth N],  PA [auth H],  PB [auth N],  QA [auth H],  R [auth A],  RA [auth I],  S [auth A],  SB [auth O],  T [auth A],  TA [auth I],  UA [auth I],  VB [auth P],  W [auth B],  XA [auth J],  Y [auth C],  YA [auth J],  Z [auth C],  ZA [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
WB [auth P]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
AB [auth K] , BA [auth D] , EA [auth E] , FB [auth L] , GA [auth F] , IB [auth M] , KA [auth G] , NB [auth N] , 
AB [auth K],  BA [auth D],  EA [auth E],  FB [auth L],  GA [auth F],  IB [auth M],  KA [auth G],  NB [auth N],  OA [auth H],  Q [auth A],  RB [auth O],  SA [auth I],  UB [auth P],  V [auth B],  WA [auth J],  X [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.79α = 90
b = 225.79β = 90
c = 225.79γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALAdata scaling
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations, Refinement description