8ZST | pdb_00008zst

Lysozyme Crystallized with Bioassembler on Earth


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

  • DOI: https://doi.org/10.1038/s41526-025-00477-w
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DO3
Query on DO3

Download Ideal Coordinates CCD File 
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
GD
Query on GD

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
F [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
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
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.03α = 90
b = 77.03β = 90
c = 38.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher Education of the Russian FederationRussian FederationNo. 075-15- 2021-1354

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references