1IES | pdb_00001ies

TETRAGONAL CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN

• PDB DOI: https://doi.org/10.2210/pdb1IES/pdb

• Classification: IRON STORAGE
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 1996-05-28 Released: 1997-01-11 
• Deposition Author(s): Granier, T., Gallois, B., Dautant, A., Langlois D'Estaintot, B., Precigoux, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Comparison of the structures of the cubic and tetragonal forms of horse-spleen apoferritin.

Granier, T., Gallois, B., Dautant, A., Langlois d'Estaintot, B., Precigoux, G.

(1997) Acta Crystallogr D Biol Crystallogr 53: 580-587

• PubMed: 15299889 
• DOI: https://doi.org/10.1107/S0907444997003314
• Primary Citation Related Structures: 
  1IER, 1IES


• PubMed Abstract: 
  

  Horse-spleen apoferritin is known to crystallize in three different space groups, cubic F432, tetragonal P42(1)2 and orthorhombic P2(1)2(1)2. A structure comparison of the cubic and tetragonal forms is presented here. Both crystal forms were obtained by the vapor-diffusion technique and data were collected at 2.26 A (cubic crystal) and 2.60 A (tetragonal crystal) resolution. Two main differences were observed between these crystal structures: (i) whereas intermolecular contacts only involve salt-bridge type interactions via cadmium ions in the cubic structure, two types of interactions are observed in the tetragonal crystal (cadmium-ion-mediated salt bridges and hydrogen-bonding interactions) and (ii) cadmium ions bound in the threefold axes of ferritin molecules exhibit lower site-occupation factors in the tetragonal structure than in the cubic one.

---

Organizational Affiliation: 
• Unité de Biophysique Structurale, EP534 CNRS, Université Bordeaux 1, Talence, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 119.8 kDa 
• Atom Count: 8,665 
• Modeled Residue Count: 1,044 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERRITIN	A, B, C, D, E, F	174	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	G [auth A], H [auth B], I [auth B], J [auth D], K [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.229	α = 90
b = 147.229	β = 90
c = 152.576	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
XDS	data reduction
MARSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-11 
Deposition Author(s): Granier, T., Gallois, B., Dautant, A., Langlois D'Estaintot, B., Precigoux, G.

Revision History  

• Version 1.0: 1997-01-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection