7VT2

Azumapecten Farreri ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural comparison between the DNA-protective ability of scallop and shrimp ferritin from iron-induced oxidative damage.

Zhang, C.Liu, Y.Zhang, T.Lv, C.Zang, J.Zhao, G.

(2022) Food Chem 386: 132827-132827

  • DOI: https://doi.org/10.1016/j.foodchem.2022.132827
  • Primary Citation of Related Structures:  
    7VT2

  • PubMed Abstract: 

    The structure and function of ferritin from seafood has been largely unexplored. In this study, homopolymeric scallop ferritin (ApF) was prepared for the first time, the apo form of which exhibited the stronger ability to protect DNA from iron-induced oxidative damage as compared to its analogue, homopolymeric shrimp ferritin (MjF). Their difference in DNA-protective activity was derived from less hydroxyl radicals produced during iron oxidation in the presence of scallop ferritin than shrimp ferritin. The kinetic results showed that apo-ApF catalyzed the faster ferrous ions oxidation by oxygen into nontoxic ferric ions as compared to apo-MjF. Newly reported crystal structure of ApF revealed that its stronger ferroxidase activity stemmed from different structures in the triple axis channel and ferroxidase site as compared to MjF. All these new findings advance our understanding of the relationship between the structure and function of food-related protein.


  • Organizational Affiliation

    College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin171Azumapecten farreriMutation(s): 0 
EC: 1.16.3.1
UniProt
Find proteins for A0A173CSP7 (Azumapecten farreri)
Explore A0A173CSP7 
Go to UniProtKB:  A0A173CSP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173CSP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
AB [auth I]
AC [auth j]
AD [auth H]
AE [auth h]
BB [auth I]
AB [auth I],
AC [auth j],
AD [auth H],
AE [auth h],
BB [auth I],
BC [auth j],
BD [auth H],
BE [auth n],
CB [auth O],
CC [auth k],
CD [auth J],
CE [auth n],
DB [auth O],
DC [auth k],
DD [auth J],
DE [auth p],
EB [auth V],
EC [auth l],
ED [auth K],
EE [auth p],
FB [auth V],
FC [auth l],
FD [auth K],
FE [auth r],
GB [auth C],
GC [auth m],
GD [auth L],
GE [auth r],
HB [auth C],
HC [auth m],
HD [auth L],
HE [auth t],
IB [auth Q],
IC [auth o],
ID [auth M],
IE [auth t],
JB [auth Q],
JC [auth o],
JD [auth M],
JE [auth u],
KB [auth U],
KC [auth q],
KD [auth N],
KE [auth u],
LB [auth U],
LC [auth q],
LD [auth N],
LE [auth x],
MB [auth a],
MC [auth w],
MD [auth P],
ME [auth x],
NB [auth a],
NC [auth w],
ND [auth P],
OB [auth c],
OC [auth s],
OD [auth R],
PB [auth c],
PC [auth s],
PD [auth R],
QB [auth d],
QC [auth v],
QD [auth T],
RB [auth d],
RC [auth v],
RD [auth T],
SB [auth e],
SC [auth B],
SD [auth W],
TB [auth e],
TC [auth B],
TD [auth W],
UB [auth f],
UC [auth D],
UD [auth X],
VB [auth f],
VC [auth D],
VD [auth Z],
WA [auth A],
WB [auth g],
WC [auth E],
WD [auth Z],
XA [auth A],
XB [auth g],
XC [auth E],
XD [auth b],
YA [auth S],
YB [auth i],
YC [auth F],
YD [auth b],
ZA [auth S],
ZB [auth i],
ZC [auth F],
ZD [auth h]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.535α = 90
b = 169.579β = 95.73
c = 198.374γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description