5J9V | pdb_00005j9v

Ten minutes iron loaded Rana Catesbeiana H' ferritin variant E57A/E136A/D140A

• PDB DOI: https://doi.org/10.2210/pdb5J9V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aquarana catesbeiana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-11 Released: 2016-10-05 
• Deposition Author(s): Pozzi, C., Di Pisa, F., Mangani, S., Bernacchioni, C., Turano, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory-Iron-Binding Sites in the Catalytic Cavity.

Bernacchioni, C., Pozzi, C., Di Pisa, F., Mangani, S., Turano, P.

(2016) Chemistry 22: 16213-16219

• PubMed: 27650996 
• DOI: https://doi.org/10.1002/chem.201602842
• Primary Citation Related Structures: 
  5J8S, 5J8W, 5J93, 5J9V, 5JAC


• PubMed Abstract: 
  

  Ferritins are iron-storage nanocage proteins that catalyze the oxidation of Fe ²⁺ to Fe ³⁺ at ferroxidase sites. By a combination of structural and spectroscopic techniques, Asp140, together with previously identified Glu57 and Glu136, is demonstrated to be an essential residue to promote the iron oxidation at the ferroxidase site. However, the presence of these three carboxylate moieties in close proximity to the catalytic centers is not essential to achieve binding of the Fe ²⁺ substrate to the diferric ferroxidase sites with the same coordination geometries as in the wild-type cages.

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Organizational Affiliation: 
• CERM and Department of Chemistry, University of Florence, Via Sacconi 6 Sesto Fiorentino, Firenze, 50019, Italy.
Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena, 53100, Italy.
Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena, 53100, Italy. [e-mail].
CERM and Department of Chemistry, University of Florence, Via Sacconi 6 Sesto Fiorentino, Firenze, 50019, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.6 kDa 
• Atom Count: 1,899 
• Modeled Residue Count: 171 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin, middle subunit	A	176	Aquarana catesbeiana	Mutation(s): 3  EC: 1.16.3.1
UniProt
Find proteins for P07798 (Aquarana catesbeiana) Explore P07798  Go to UniProtKB:  P07798

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.744	α = 90
b = 183.744	β = 90
c = 183.744	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Pozzi, C., Di Pisa, F., Mangani, S., Bernacchioni, C., Turano, P.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references
• Version 1.2: 2017-11-29
  Changes: Database references
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 1.4: 2019-02-20
  Changes: Data collection, Derived calculations
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description