5CZU | pdb_00005czu

Crystal structure of FeCat-Fn

• PDB DOI: https://doi.org/10.2210/pdb5CZU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-01 Released: 2015-11-18 
• Deposition Author(s): Abe, S., Nakajima, H., Kondo, M., Nakane, T., Nakao, T., Ueno, T., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Construction of an enterobactin analogue with symmetrically arranged monomer subunits of ferritin

Nakajima, H., Kondo, M., Nakane, T., Abe, S., Nakao, T., Watanabe, Y., Ueno, T.

(2015) Chem Commun (Camb) 51: 16609-16612

• PubMed: 26404005 
• DOI: https://doi.org/10.1039/c5cc06904a
• Primary Citation Related Structures: 
  5AXS, 5CZU


• PubMed Abstract: 
  

  A set of three catecholamide ligands mimicking the structure of enterobactin was constructed on ferritin, where the 3-fold symmetric arrangement of the monomer subunits served as a foundation to form a coordination space. Similar to enterobactin, the ligands showed strong affinity for the ferric ion and formed a tris-catechoyl complex. Crystallography revealed that the complex was embedded in the entrance of the 3-fold axis channel.

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Organizational Affiliation: 
• Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Osaka, 558-8585, Japan. [e-mail].

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 (software)

Macromolecule Content 

• Total Structure Weight: 20.84 kDa 
• Atom Count: 1,652 
• Modeled Residue Count: 174 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	174	Equus caballus	Mutation(s): 2  Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4LF	B [auth A]	N-[2-[2,5-bis(oxidanylidene)pyrrol-1-yl]ethyl]-2,3-bis(oxidanyl)benzamide C13 H12 N2 O5 BABSFPLAEBUXOA-UHFFFAOYSA-N
CD	D [auth A], E [auth A], F [auth A], G [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	H [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.208 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.07	α = 90
b = 181.07	β = 90
c = 181.07	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Abe, S., Nakajima, H., Kondo, M., Nakane, T., Nakao, T., Ueno, T., Watanabe, Y.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2015-11-25
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary