7OPV | pdb_00007opv

Crystal structure of the computationally designed SAKe6BE-3HH protein, alternative packing

• PDB DOI: https://doi.org/10.2210/pdb7OPV/pdb

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


• Deposited: 2021-06-01 Released: 2022-12-14 
• Deposition Author(s): Wouters, S.M.L., Noguchi, H., 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: 1.95 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: in silico

Literature

Design and Characterization of SAKe, a Building Block for Protein Self-Assembly

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

(2026) ACS Nano 

• DOI: https://doi.org/10.1021/acsnano.6c04954

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.86 kDa 
• Atom Count: 4,547 
• Modeled Residue Count: 562 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAKe6BE-3HH	A, B	286	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.961	α = 72.18
b = 47.152	β = 76.4
c = 70.876	γ = 60.18

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Wouters, S.M.L., Noguchi, H., 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
• Version 1.2: 2026-07-29
  Changes: Database references, Structure summary