8ZBO | pdb_00008zbo

Crystal structure of the biphotochromic fluorescent protein moxSAASoti (F97M variant) in its green on-state

PDB DOI: https://doi.org/10.2210/pdb8ZBO/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Stylocoeniella armata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-26 Released: 2024-06-12
Deposition Author(s): Boyko, K.M., Matyuta, I.O., Marynich, N.K., Minyaev, M.E., Khadiyatova, A.A., Popov, V.O., Savitsky, A.P.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.231 (Depositor), 0.195 (DCC)
R-Value Work:
0.178 (Depositor), 0.189 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Single-point substitution F97M leads to in cellulo crystallization of the biphotochromic protein moxSAASoti.

Marynich, N.K., Boyko, K.M., Matyuta, I.O., Minyaev, M.E., Khadiyatova, A.A., Popov, V.O., Savitsky, A.P.

(2024) Biochem Biophys Res Commun 732: 150419-150419

PubMed: 39032411 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2024.150419
Primary Citation Related Structures:
8ZBO

PubMed Abstract:
To enhance the photoconversion performance of biphotochromic moxSAASoti protein, a substitution F97 M was introduced. In addition to enhancing the target properties, this substitution also resulted in the crystallization of the recombinant protein within living HeLa cells (also referred to as in cellulo crystallization). The phenomenon of protein crystallization in living cells is not unique, yet the mechanisms and application of in cellulo crystallization remain significant for further research. However, in cellulo crystallization is atypical for fluorescent proteins and detrimental for their biotechnological application. The objective of this study was to elucidate the underlying mechanisms responsible for the crystallization of moxSAASoti ^F97Min cellulo. For this purpose, the crystal structure of the green form of biphotochromic protein moxSAASoti ^F97M was determined at high resolution, which surprisingly has a space group, different from those of parent mSAASoti ^C21N. The analysis provided allowed to propose a mechanism of new crystal contacts formation, which might be a cause of in cellulo protein crystallization.

Organizational Affiliation

A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, Russia.

Macromolecule Content

Total Structure Weight: 51 kDa
Atom Count: 3,661
Modeled Residue Count: 416
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F97M variant of the biphotochromic fluorescent protein moxSAASoti	A [auth C], B [auth A]	221	Stylocoeniella armata	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C]	G [auth C], H [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain G [auth C] Focus chain H [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain F [auth C] SDF format, chain E [auth C] SDF format, chain D [auth C] SDF format, chain C MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] MOL2 format, chain D [auth C] MOL2 format, chain C mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C] mmCIF format, chain D [auth C] mmCIF format, chain C	C D [auth C] E [auth C] F [auth C] I [auth A] C, D [auth C], E [auth C], F [auth C], I [auth A], J [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain I [auth A] Focus chain J [auth A]