5CHB | pdb_00005chb

Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal

PDB DOI: https://doi.org/10.2210/pdb5CHB/pdb
Entry: 5CHB supersedes: 4ZCO

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2015-07-10 Released: 2015-07-22
Deposition Author(s): Voet, A.R.D., Noguchi, H., Addy, C., Zhang, K.Y.J., Tame, J.R.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.188 (Depositor), 0.193 (DCC)
R-Value Work:
0.152 (Depositor), 0.162 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

PubMed: 26136355 Search on PubMed
DOI: https://doi.org/10.1002/anie.201503575
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 27.43 kDa
Atom Count: 2,014
Modeled Residue Count: 254
Deposited Residue Count: 261
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nvPizza2-S16H58	A, B, C	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A] E [auth B] F [auth B] G [auth B] L [auth C] D [auth A], E [auth B], F [auth B], G [auth B], L [auth C], M [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth C] Focus chain M [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B] I [auth B] J [auth B] N [auth C] O [auth C] H [auth B], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.188 (Depositor), 0.193 (DCC)
R-Value Work: 0.152 (Depositor), 0.162 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.2	α = 90
b = 61.2	β = 90
c = 109.558	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-07-22

Deposition Author(s):

This entry supersedes: 4ZCO

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