8GOI | pdb_00008goi

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.281 (Depositor), 0.281 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth G] SDF format, chain I [auth B] MOL2 format, chain J [auth G] MOL2 format, chain I [auth B] mmCIF format, chain J [auth G] mmCIF format, chain I [auth B]	I [auth B], J [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth G] Interactions & Density Focus chain I [auth B] Focus chain J [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.281 (Depositor), 0.281 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.228 (Depositor)

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAC1304

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.