3AF8 | pdb_00003af8

Crystal Structure of Pd(ally)/apo-C126AFr

PDB DOI: https://doi.org/10.2210/pdb3AF8/pdb

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

Deposited: 2010-02-24 Released: 2010-08-11
Deposition Author(s): Abe, S., Hikage, T., Watanabe, Y., Kitagawa, S., Ueno, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.195 (Depositor), 0.193 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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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

PubMed: 20586408 Search on PubMed
DOI: https://doi.org/10.1021/ic1003758
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 21 kDa
Atom Count: 1,697
Modeled Residue Count: 172
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A [auth X]	174	Equus caballus	Mutation(s): 1 Gene Names: FTL
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791 Go to UniProtKB: P02791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLL Query on PLL Download:Ideal Coordinates CCD File SDF format, chain F [auth X] SDF format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X]	F [auth X], G [auth X]	Palladium(II) allyl complex C₃ H₅ Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N		Interactions Focus chain F [auth X] Focus chain G [auth X] Interactions & Density Focus chain F [auth X] Focus chain G [auth X]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain B [auth X] SDF format, chain C [auth X] SDF format, chain D [auth X] MOL2 format, chain B [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] mmCIF format, chain B [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X]	B [auth X], C [auth X], D [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X] mmCIF format, chain E [auth X]	E [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] SDF format, chain K [auth X] SDF format, chain L [auth X] SDF format, chain M [auth X] SDF format, chain N [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] MOL2 format, chain M [auth X] MOL2 format, chain N [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X] mmCIF format, chain M [auth X] mmCIF format, chain N [auth X]	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		Interactions Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Interactions & Density Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X]