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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/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 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
bacterioferritin
A, B, C, D, E
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / 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
3PY
Query on 3PY
Download Ideal Coordinates CCD File 
RA [auth D]3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
SO4
Query on SO4
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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
GOL
Query on GOL
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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
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
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description