3NP2

Crystal Structure of Pd(allyl)/apo-E45C/C48A-rHLFr

• PDB DOI: https://doi.org/10.2210/pdb3NP2/pdb

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


• Deposited: 2010-06-27 Released: 2010-12-22 
• Deposition Author(s): Wang, Z., Ueno, T., Abe, S., Takezawa, Y., Aoyagi, H., Hikage, T., Watanabe, Y., Kitagawa, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin.

Wang, Z., Takezawa, Y., Aoyagi, H., Abe, S., Hikage, T., Watanabe, Y., Kitagawa, S., Ueno, T.

(2011) Chem Commun (Camb) 47: 170-172

• PubMed: 20730233 
• DOI: https://doi.org/10.1039/c0cc02221g
• Primary Citation of Related Structures:  
  3NOZ, 3NP0, 3NP2


• PubMed Abstract: 
  

  Apo-ferritin (apo-Fr) mutants are used as scaffolds to accommodate palladium (allyl) complexes. Various coordination arrangements of the Pd complexes are achieved by adjusting the positions of cysteine and histidine residues on the interior surface of the apo-Fr cage.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Nagoya, 464-8602, 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: 21.14 kDa 
• Atom Count: 1,637 
• 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 [auth X]	174	Equus caballus	Mutation(s): 2
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791  Go to UniProtKB:  P02791

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLL	C [auth X], D [auth X]	Palladium(II) allyl complex C3 H5 Pd WTWGCTVOVPTEEU-UHFFFAOYSA-N
CD	G [auth X], H [auth X]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PD	E [auth X], F [auth X]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N
SO4	B [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth X], J [auth X], K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.229 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.296	α = 90
b = 182.296	β = 90
c = 182.296	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Wang, Z., Ueno, T., Abe, S., Takezawa, Y., Aoyagi, H., Hikage, T., Watanabe, Y., Kitagawa, S.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description