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


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 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],
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],
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],
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],
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



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: 2017-10-11
    Changes: Refinement description