7ONA | pdb_00007ona

Crystal structure of the computationally designed SAKe6AC protein

• PDB DOI: https://doi.org/10.2210/pdb7ONA/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-25 Released: 2022-12-14 
• Deposition Author(s): Wouters, S.M.L., Noguchi, H., Velpula, G., Clarke, D.E., Voet, A.R.D., De Feyter, S.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: in silico

Literature

SAKe: Computationally Designed Modular Protein Building Blocks for Macromolecular Assemblies

Wouters, S.M.L., Clarke, D.E., Noguchi, H., Velpula, G., Voet, A.R.D., De Feyter, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.87 kDa 
• Atom Count: 2,363 
• Modeled Residue Count: 277 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAKe6AC	A	310	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.38	α = 90
b = 74.873	β = 122.08
c = 46.938	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Wouters, S.M.L., Noguchi, H., Velpula, G., Clarke, D.E., Voet, A.R.D., De Feyter, S.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1S89918N
Research Foundation - Flanders (FWO)	Belgium	G0F9316N
Research Foundation - Flanders (FWO)	Belgium	G051917N

Revision History  

• Version 1.0: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description