5CHB

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 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/anie.201503575
  • Also Cited By: 5F53

  • 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 ...

    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.,Drug Design Laboratory, Yokohama City University, 1-7-29, Suehiro, Tsurumi, Yokohama, 230-0045 (Japan).,Drug Design Laboratory, Yokohama City University, 1-7-29, Suehiro, Tsurumi, Yokohama, 230-0045 (Japan). jtame@tsurumi.yokohama-cu.ac.jp.,Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045 (Japan). kamzhang@riken.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nvPizza2-S16H58
A, B, C
87N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.200α = 90.00
b = 61.200β = 90.00
c = 109.558γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 1.2: 2017-10-04
    Type: Data collection, Database references, Derived calculations