8GOI

23-residues Heterotetramic Antiparallel Coiled-Coil Derived From LacI

• PDB DOI: https://doi.org/10.2210/pdb8GOI/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-25 Released: 2023-08-30 
• Deposition Author(s): Kumasaka, T.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.281 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

Literature

Design of interchain Glu-Arg salt-bridges stabilizing heterotetrameric coiled-coil derived from Lac repressor.

Otsuka, Y., Osaki, A., Nakamura, Y., Mizuno, N., Kawamura, T., Hasegawa, K., Yamaguchi, H., Kumasaka, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.32 kDa 
• Atom Count: 1,457 
• Modelled Residue Count: 178 
• Deposited Residue Count: 184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lac23ys_aEE, an acidic mutant of LacI C-terminal tetramerization helix	A, C, E, G	23	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lac23ys_bRR, a basic mutant of LacI C-terminal tetramerization helix	B, D, F, H	23	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B], J [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.281 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.967	α = 90
b = 42.973	β = 90
c = 85.923	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Kumasaka, T.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAC1304

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release