5CHB | pdb_00005chb

Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein

Voet, A.R.D., Noguchi, H., Addy, C., Zhang, K.Y.J., Tame, J.R.H.

(2015) Angew Chem Int Ed Engl 54: 9857-9860

  • DOI: https://doi.org/10.1002/anie.201503575
  • Primary Citation of Related Structures:  
    5CHB

  • PubMed Abstract: 

    We have engineered a metal-binding site into the novel artificial β-propeller protein Pizza. This new Pizza variant carries two nearly identical domains per polypeptide chain, and forms a trimer with three-fold symmetry. The designed single metal ion binding site lies on the symmetry axis, bonding the trimer together. Two copies of the trimer associate in the presence of cadmium chloride in solution, and very high-resolution X-ray crystallographic analysis reveals a nanocrystal of cadmium chloride, sandwiched between two trimers of the protein. This nanocrystal, containing seven cadmium ions lying in a plane and twelve interspersed chloride ions, is the smallest reported to date. Our results indicate the feasibility of using rationally designed symmetrical proteins to biomineralize nanocrystals with useful properties.

    • Organizational Affiliation: 

    Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045 (Japan). arnout.voet@riken.jp.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nvPizza2-S16H58
A, B, C
87synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD
Download Ideal Coordinates CCD File 
D [auth A]
E [auth B]
F [auth B]
G [auth B]
L [auth C]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL
Download Ideal Coordinates CCD File 
H [auth B]
I [auth B]
J [auth B]
N [auth C]
O [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.2α = 90
b = 61.2β = 90
c = 109.558γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2017-10-04
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description