7DNS | pdb_00007dns

Crystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de novo designed protein with an asymmetric all-alpha topology

• PDB DOI: https://doi.org/10.2210/pdb7DNS/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-10 Released: 2021-07-28 
• Deposition Author(s): Suzuki, K., Kobayashi, N., Murata, T., Sakuma, K., Kosugi, T., Koga, R., Koga, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Design of complicated all-alpha protein structures

Sakuma, K., Kobayashi, N., Sugiki, T., Nagashima, T., Fujiwara, T., Suzuki, K., Kobayashi, N., Murata, T., Kosugi, T., Koga, R., Koga, N.

(2024) Nat Struct Mol Biol 

• DOI: https://doi.org/10.1038/s41594-023-01147-9

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.5 kDa 
• Atom Count: 1,443 
• Modeled Residue Count: 178 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
de novo designed protein	A, B	97	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.98	α = 90
b = 33.66	β = 93.11
c = 58.38	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Suzuki, K., Kobayashi, N., Murata, T., Sakuma, K., Kosugi, T., Koga, R., Koga, N.

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 2.0: 2021-10-06
  Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references
• Version 2.2: 2024-01-10
  Changes: Database references