3AF9

Crystal Structure of Pd(allyl)/apo-C48AFr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin.

Abe, S.Hikage, T.Watanabe, Y.Kitagawa, S.Ueno, T.

(2010) Inorg Chem 49: 6967-6973

  • DOI: https://doi.org/10.1021/ic1003758
  • Primary Citation of Related Structures:  
    3AF7, 3AF8, 3AF9

  • PubMed Abstract: 

    Hybridization of metal complexes and protein scaffolds is an important subject in bioinorganic chemistry and materials science. Efforts to provide non-natural functions to proteins will likely lead to advances in development of catalysts, sensors, and so on. Mechanistic investigations of the process of binding of metal complexes within protein scaffolds and characterization of the resulting coordination structures will help us to design and control coordination structures of metal complexes for construction of hybrid proteins containing metal complexes. In this work, the processes of accumulation and incorporation of organometallic palladium complexes within the cage of the iron storage protein apo-ferritin (apo-Fr) are elucidated by analysis of X-ray crystal structures of apo-Fr and selected mutants thereof, in the presence of the metal complexes. The crystal structure of apo-Fr containing Pd(allyl) (allyl = eta(3)-C(3)H(5)) complexes shows that thiolato-bridged dinuclear Pd(allyl) complexes are formed at two binding sites within the cage of apo-Fr. The crystal structures of apo-Fr and its Cys- and His-deletion mutants containing Pd(allyl) complexes indicate that Cys126 accelerates the incorporation of Pd(allyl) complexes into the cage. In addition, Cys48 and Cys126 are essential for accumulation of Pd(allyl) complexes and stabilizing the square planar coordination structure.


  • Organizational Affiliation

    Institute for Integrated Cell-Material Sciences (iCeMS), Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin light chainA [auth X]174Equus caballusMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLL
Query on PLL

Download Ideal Coordinates CCD File 
F [auth X]Palladium(II) allyl complex
C3 H5 Pd
WTWGCTVOVPTEEU-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth X],
D [auth X],
E [auth X]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PD
Query on PD

Download Ideal Coordinates CCD File 
G [auth X]PALLADIUM ION
Pd
MUJIDPITZJWBSW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth X]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth X]
I [auth X]
J [auth X]
K [auth X]
L [auth X]
H [auth X],
I [auth X],
J [auth X],
K [auth X],
L [auth X],
M [auth X],
N [auth X]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.433α = 90
b = 182.433β = 90
c = 182.433γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description