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 
  • R-Value Observed: 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 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEC
Query on FEC

Download Ideal Coordinates CCD File 
AE [auth P], BD [auth L], EA [auth B], EC [auth I], GB [auth F], GD [auth M], OB [auth G], SA [auth D]1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
C36 H36 Fe N4 O8
FEDZMOFKVKOYTI-RGGAHWMASA-L
 Ligand Interaction
3PY
Query on 3PY

Download Ideal Coordinates CCD File 
RA [auth D]3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AC [auth I] , AD [auth L] , BA [auth B] , BC [auth I] , CA [auth B] , CC [auth I] , DA [auth B] , DB [auth F] , 
AC [auth I],  AD [auth L],  BA [auth B],  BC [auth I],  CA [auth B],  CC [auth I],  DA [auth B],  DB [auth F],  DC [auth I],  EB [auth F],  ED [auth M],  FB [auth F],  FD [auth M],  JA [auth C],  JC [auth J],  KA [auth C],  KC [auth J],  LA [auth C],  LB [auth G],  LC [auth J],  LD [auth N],  MB [auth G],  MD [auth N],  NB [auth G],  ND [auth N],  OC [auth K],  PA [auth D],  QA [auth D],  RC [auth K],  RD [auth O],  S [auth A],  SC [auth K],  SD [auth O],  T [auth A],  TB [auth H],  TC [auth K],  U [auth A],  UA [auth E],  UB [auth H],  V [auth A],  VB [auth H],  W [auth A],  XA [auth E],  XC [auth L],  XD [auth P],  Y [auth B],  YA [auth E],  YC [auth L],  YD [auth P],  ZC [auth L],  ZD [auth P]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth E] , BE [auth P] , FA [auth B] , FC [auth I] , GA [auth B] , GC [auth I] , HB [auth F] , HD [auth M] , 
AB [auth E],  BE [auth P],  FA [auth B],  FC [auth I],  GA [auth B],  GC [auth I],  HB [auth F],  HD [auth M],  IB [auth F],  ID [auth M],  MA [auth C],  MC [auth J],  NC [auth J],  OD [auth N],  PB [auth G],  QB [auth G],  TA [auth D],  TD [auth O],  UC [auth K],  UD [auth O],  WB [auth H],  X [auth A],  XB [auth H],  ZA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
AA [auth B] , BB [auth F] , CB [auth F] , CD [auth M] , DD [auth M] , HA [auth C] , HC [auth J] , IA [auth C] , 
AA [auth B],  BB [auth F],  CB [auth F],  CD [auth M],  DD [auth M],  HA [auth C],  HC [auth J],  IA [auth C],  IC [auth J],  JB [auth G],  JD [auth N],  KB [auth G],  KD [auth N],  NA [auth D],  OA [auth D],  PC [auth K],  PD [auth O],  Q [auth A],  QC [auth K],  QD [auth O],  R [auth A],  RB [auth H],  SB [auth H],  VA [auth E],  VC [auth L],  VD [auth P],  WA [auth E],  WC [auth L],  WD [auth P],  YB [auth I],  Z [auth B],  ZB [auth I]
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 
  • R-Value Observed: 0.214 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.3α = 90
b = 225.3β = 90
c = 225.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SnBphasing
MLPHAREphasing
DMmodel building
SHELXL-97refinement
CCP4data scaling
DMphasing

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: 2008-05-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description