3NP0

Crystal Structure of Pd(allyl)/apo-E45C/H49A/R52H-rHLFr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Nagoya, 464-8602, 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): 3 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLL
Query on PLL

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

Download Ideal Coordinates CCD File 
J [auth X]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
K [auth X]
L [auth X]
M [auth X]
N [auth X]
O [auth X]
K [auth X],
L [auth X],
M [auth X],
N [auth X],
O [auth X],
P [auth X],
Q [auth X],
R [auth X]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.959α = 90
b = 180.959β = 90
c = 180.959γ = 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: 2010-12-22
    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