1NFV

X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

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.Mol.Biol. 10: 285-290

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

  • 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 ...

    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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
bacterioferritin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
179Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Gene Names: bfr
EC: 1.16.3.1
Find proteins for Q93PP9 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  Q93PP9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, M, N, O, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3PY
Query on 3PY

Download SDF File 
Download CCD File 
D
3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
 Ligand Interaction
FEC
Query on FEC

Download SDF File 
Download CCD File 
B, D, F, G, I, L, M, P
1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
FE-COPROPORPHYRIN III
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 225.300α = 90.00
b = 225.300β = 90.00
c = 225.300γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
CCP4data scaling
DMphasing
DENZOdata reduction
DMmodel building
SHELXL-97refinement
SCALAdata scaling
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-05-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description