3O7R | pdb_00003o7r

Crystal structure of Ru(p-cymene)/apo-H49AFr

• PDB DOI: https://doi.org/10.2210/pdb3O7R/pdb

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


• Deposited: 2010-07-31 Released: 2011-04-20 
• Deposition Author(s): Takezawa, Y., Bockmann, P., Sugi, N., Wang, Z., Abe, S., Murakami, T., Hikage, T., Erker, G., Watanabe, Y., Kitagawa, S., Ueno, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Incorporation of organometallic Ru complexes into apo-ferritin cage.

Takezawa, Y., Bockmann, P., Sugi, N., Wang, Z., Abe, S., Murakami, T., Hikage, T., Erker, G., Watanabe, Y., Kitagawa, S., Ueno, T.

(2011) J Chem Soc ,dalton Trans 40: 2190-2195

• PubMed: 21113534 
• DOI: https://doi.org/10.1039/c0dt00955e
• Primary Citation Related Structures: 
  3O7R, 3O7S


• PubMed Abstract: 
  

  Spherical protein cages such as an iron storage protein, ferritin, have great potential as nanometer-scale capsules to assemble and store metal ions and complexes. We report herein the synthesis of a composite of an apo-ferritin cage and Ru(p-cymene) complexes. Ru complexes were efficiently incorporated into the ferritin cavity without degradation of its cage structure. X-Ray crystallography revealed that the Ru complexes were immobilized on the interior surface of the cage mainly by the coordination of histidine residues.

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Organizational Affiliation: 
• Research Center for Materials Science, Nagoya University, Furo-cho, Nagoya, Japan.

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: 20.89 kDa 
• Atom Count: 1,640 
• Modeled Residue Count: 173 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
RU	E [auth A], F [auth A]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.703	α = 90
b = 181.703	β = 90
c = 181.703	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Takezawa, Y., Bockmann, P., Sugi, N., Wang, Z., Abe, S., Murakami, T., Hikage, T., Erker, G., Watanabe, Y., Kitagawa, S., Ueno, T.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations