5E2D

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • 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. tueno@bio.titech.ac.jp.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chain174Equus caballusMutation(s): 0 
Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus)
Explore P02791 
Go to UniProtKB:  P02791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02791
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IR
Query on IR
Download Ideal Coordinates CCD File 
G [auth A]IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
IR3
Query on IR3
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B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]		IRIDIUM (III) ION
Ir
MILUBEOXRNEUHS-UHFFFAOYSA-N
PLL
Query on PLL
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J [auth A],
K [auth A]		Palladium(II) allyl complex
C3 H5 Pd
WTWGCTVOVPTEEU-UHFFFAOYSA-N
CD
Query on CD
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M [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PD
Query on PD
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L [auth A]PALLADIUM ION
Pd
MUJIDPITZJWBSW-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
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 = 181.19α = 90
b = 181.19β = 90
c = 181.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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