5I1Y | pdb_00005i1y

NvPizza2-H16S58 with cobalt

• PDB DOI: https://doi.org/10.2210/pdb5I1Y/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-02-07 Released: 2017-02-08 
• Deposition Author(s): Tame, J.R.H., Voet, A.R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

NvPizza2-H16S58 with cobalt

Tame, J.R.H., Voet, A.R.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.89 kDa 
• Atom Count: 1,917 
• Modeled Residue Count: 257 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nvPizz2a-H16S58	A, B, C	87	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	G [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.453	α = 90
b = 69.453	β = 90
c = 187.264	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Tame, J.R.H., Voet, A.R.D.

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description