8ZST | pdb_00008zst

Lysozyme Crystallized with Bioassembler on Earth

PDB DOI: https://doi.org/10.2210/pdb8ZST/pdb
Entry: 8ZST supersedes: 8RT2

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2024-06-05 Released: 2025-05-28
Deposition Author(s): MacCarthy, C., Koudan, E.V., Petrov, S.V., Levin, A.A., Khesuani, Y.D., Borshchevskiy, V.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.80 Å
R-Value Free:
0.133 (Depositor), 0.137 (DCC)
R-Value Work:
0.121 (Depositor), 0.127 (DCC)
R-Value Observed:
0.122 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Exploring the potential of a bioassembler for protein crystallization in space.

MacCarthy, C., Koudan, E., Shevtsov, M., Parfenov, V., Petrov, S., Levin, A., Senatov, F., Sykilinda, N., Ostrovskiy, S., Pekov, S., Gushchin, I., Popov, I., Zinovev, E., Bogorodskiy, A., Mishin, A., Ivanovich, V., Rogachev, A., Khesuani, Y., Borshchevskiy, V.

(2025) NPJ Microgravity 11: 25-25

PubMed: 40517138 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41526-025-00477-w
Primary Citation Related Structures:
8ZST, 8ZSU

PubMed Abstract:
Protein crystallization holds paramount significance in structural biology, serving as a pivotal technique for unveiling the three-dimensional (3D) architecture of proteins. While microgravity conditions in space offer distinct advantages for high-quality protein crystal growth by mitigating the influences of gravity and convection, the development of reliable techniques for protein crystallization in space with precise control over the crystallization process and its meticulous inspections remains a challenge. In this study, we present an innovative bioassembler-specifically, the 'Organ.Aut'-which we successfully employed to crystallize protein in space. The bioassembler 'Organ.Aut' produced highly ordered crystals diffracted to a true-atomic resolution of ∼1 Å. These data allowed for a detailed examination of atomic structures, enabling thorough structural comparisons with crystals grown on Earth. Our finding suggests that the bioassembler 'Organ.Aut' stands as a promising and viable option for advancing protein crystallization in space.

Organizational Affiliation

Moscow Institute of Physics and Technology, Dolgoprudny, Russia.

Macromolecule Content

Total Structure Weight: 15.75 kDa
Atom Count: 1,585
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DO3 Query on DO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID C₁₇ H₃₂ N₄ O₇ IQUHNCOJRJBMSU-CQSZACIVSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]
GD Query on GD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], D [auth A]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]