5E2D

Crystal structure of IrCp*/Pd(allyl)-apo-Fr

• PDB DOI: https://doi.org/10.2210/pdb5E2D/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Equus caballus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2016-04-20 
• Deposition Author(s): Maity, B., Fukumori, K., Abe, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartments

Maity, B., Fukumori, K., Abe, S., Ueno, T.

(2016) Chem Commun (Camb) 52: 5463-5466

• PubMed: 27021005 
• DOI: https://doi.org/10.1039/c6cc00679e
• Primary Citation of Related Structures:  
  5E1U, 5E2D, 5HQO


• PubMed Abstract: 
  

  Natural protein-based microcompartments containing multiple enzymes promote cascade reactions within cells. We use the apo-ferritin protein cage to mimic such biocompartments by immobilizing two organometallic Ir and Pd complexes into the single protein cage. Precise locations of the metals and their accumulation mechanism were studied by X-ray crystallography.

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Organizational Affiliation: 

Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, 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: 21.73 kDa 
• Atom Count: 1,556 
• Modelled Residue Count: 172 
• 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): 0  Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR	G [auth A]	IRIDIUM ION Ir MOHYGSBMXIJZBJ-UHFFFAOYSA-N
IR3	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	IRIDIUM (III) ION Ir MILUBEOXRNEUHS-UHFFFAOYSA-N
PLL	J [auth A], K [auth A]	Palladium(II) allyl complex C3 H5 Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N
CD	M [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PD	L [auth A]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.201 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.19	α = 90
b = 181.19	β = 90
c = 181.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Maity, B., Fukumori, K., Abe, S., Ueno, T.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description