7ONH | pdb_00007onh

Crystal structure of the computationally designed SAKe6BE-L3 protein

• PDB DOI: https://doi.org/10.2210/pdb7ONH/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: 1.65 Å
• R-Value Free: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.160 (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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.97 kDa 
• Atom Count: 5,506 
• Modeled Residue Count: 635 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAKe6BE-L3	A, B	325	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.624	α = 90
b = 90.624	β = 90
c = 90.663	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