8GOJ | pdb_00008goj

23-residues Heterotetramic Antiparallel Coiled-Coil Derived From LacI

• PDB DOI: https://doi.org/10.2210/pdb8GOJ/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: 1.38 Å
• R-Value Free: 
  0.258 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

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

Otsuka, Y., Kumasaka, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local 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: 10.33 kDa 
• Atom Count: 755 
• Modeled Residue Count: 88 
• Deposited Residue Count: 92 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lac23ys_EE, an acidic mutant of LacI C-terminal tetramerization helix	A, C	23	Escherichia coli	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lac23ys_KK, a basic mutant of LacI C-terminal tetramerization helix	B, D	23	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth C], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.258 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.84	α = 90
b = 41.9	β = 102.91
c = 38.84	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
  
• Version 1.1: 2026-03-04
  Changes: Refinement description, Structure summary