4REU

Revelation of Endogenously bound Fe2+ ions in the Crystal Structure of Ferritin from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Literature

Revelation of Endogenously bound Fe(2+) ions in the Crystal Structure of Ferritin from Escherichia coli.

Thiruselvam, V.Sivaraman, P.Kumarevel, T.S.Ponnuswamy, M.N.

(2014) Biochem Biophys Res Commun 

  • DOI: 10.1016/j.bbrc.2014.10.007
  • Primary Citation of Related Structures:  
    4REU

  • PubMed Abstract: 
  • Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites ...

    Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5Å. The structural analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.


    Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India. Electronic address: mnpsy2004@yahoo.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin
A, B, C, D, E, F
A, B, C, D, E, F
164Escherichia coli str. K-12 substr. MDS42Mutation(s): 0 
Gene Names: ftnECMDS42_1565
EC: 1.16.3.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
GA [auth C],
OA [auth D]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
N [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth E],
BB [auth E],
CB [auth E],
DB [auth E],
EA [auth C],
AB [auth E],
BB [auth E],
CB [auth E],
DB [auth E],
EA [auth C],
EB [auth E],
FA [auth C],
I [auth A],
J [auth A],
JB [auth F],
K [auth A],
KB [auth F],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
NA [auth D],
W [auth B],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
G [auth A],
H [auth A],
HB [auth F],
CA [auth C],
DA [auth C],
G [auth A],
H [auth A],
HB [auth F],
IB [auth F],
JA [auth D],
KA [auth D],
U [auth B],
V [auth B],
YA [auth E],
ZA [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
FB [auth E],
GB [auth E],
HA [auth C],
AA [auth B],
BA [auth B],
FB [auth E],
GB [auth E],
HA [auth C],
IA [auth C],
LB [auth F],
MB [auth F],
NB [auth F],
O [auth A],
OB [auth F],
P [auth A],
PB [auth F],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
TA [auth D],
UA [auth D],
VA [auth D],
WA [auth D],
XA [auth D],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
PA [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.998α = 90
b = 127.998β = 90
c = 170.902γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release