5F53 | pdb_00005f53

Nano-ring of cadmium ions coordinated by nvPizza2-S16S58

PDB DOI: https://doi.org/10.2210/pdb5F53/pdb

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

Deposited: 2015-12-04 Released: 2016-12-14
Deposition Author(s): Voet, A.R.D., Tame, J.R.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.210 (Depositor), 0.212 (DCC)
R-Value Work:
0.186 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A cadmium chloride ring created by a designed symmetrical protein

Voet, A.R.D., Terada, D., Noguchi, H., Addy, C., Unzai, S., Akashi, S., Zhang, K.Y.J., Tame, J.R.H.

To be published.

Macromolecule Content

Total Structure Weight: 8.95 kDa
Atom Count: 649
Modeled Residue Count: 84
Deposited Residue Count: 87
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NVPIZZA2-S16S58	A	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.210 (Depositor), 0.212 (DCC)
R-Value Work: 0.186 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.32	α = 90
b = 110.32	β = 90
c = 110.32	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Voet, A.R.D.

Tame, J.R.H.

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations