1NF4

X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


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:  
    1NF4, 1NF6, 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
bacterioferritin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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
UniProt
Find proteins for Q93PP9 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore Q93PP9 
Go to UniProtKB:  Q93PP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93PP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEC
Query on FEC

Download Ideal Coordinates CCD File 
FB [auth G],
HD [auth P],
JA [auth C],
KC [auth L],
RC [auth M],
FB [auth G],
HD [auth P],
JA [auth C],
KC [auth L],
RC [auth M],
TB [auth I],
UA [auth E],
V [auth A]
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 
AA [auth B],
AD [auth O],
BA [auth B],
BC [auth K],
BD [auth P],
AA [auth B],
AD [auth O],
BA [auth B],
BC [auth K],
BD [auth P],
CA [auth B],
CB [auth G],
CC [auth K],
DB [auth G],
DC [auth K],
EB [auth G],
ED [auth P],
FA [auth C],
FD [auth P],
GA [auth C],
GC [auth L],
GD [auth P],
HA [auth C],
HC [auth L],
IA [auth C],
IB [auth H],
IC [auth L],
JB [auth H],
JC [auth L],
KB [auth H],
LB [auth H],
MA [auth D],
MB [auth I],
NA [auth D],
NC [auth M],
OA [auth D],
OC [auth M],
PA [auth E],
PB [auth I],
PC [auth M],
QB [auth I],
QC [auth M],
RB [auth I],
S [auth A],
SA [auth E],
SB [auth I],
T [auth A],
TA [auth E],
U [auth A],
UC [auth N],
VC [auth N],
W [auth B],
WB [auth J],
WC [auth N],
XA [auth F],
XB [auth J],
YA [auth F],
YB [auth J],
Z [auth B],
ZA [auth F],
ZC [auth O]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
AB [auth G],
AC [auth K],
BB [auth G],
CD [auth P],
DA [auth C],
AB [auth G],
AC [auth K],
BB [auth G],
CD [auth P],
DA [auth C],
DD [auth P],
EA [auth C],
EC [auth L],
FC [auth L],
GB [auth H],
HB [auth H],
KA [auth D],
LA [auth D],
LC [auth M],
MC [auth M],
NB [auth I],
OB [auth I],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
SC [auth N],
TC [auth N],
UB [auth J],
VA [auth F],
VB [auth J],
WA [auth F],
X [auth B],
XC [auth O],
Y [auth B],
YC [auth O],
ZB [auth K]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.68α = 90
b = 225.68β = 90
c = 225.68γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALAdata scaling
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



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: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description