7OP4 | pdb_00007op4

Crystal structure of the computationally designed SAKe6BE-3HH protein

• PDB DOI: https://doi.org/10.2210/pdb7OP4/pdb

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


• Deposited: 2021-05-29 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: 1.52 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.185 (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: 30.43 kDa 
• Atom Count: 2,320 
• Modeled Residue Count: 280 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.049	α = 90
b = 76.29	β = 90.02
c = 67.987	γ = 90

Software Package:

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

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