9TBL | pdb_00009tbl

SSX Lysozyme at 100K

PDB DOI: https://doi.org/10.2210/pdb9TBL/pdb

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

Deposited: 2025-11-20 Released: 2026-04-22
Deposition Author(s): Bjelcic, M., Branden, G., Ghosh, S.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.

Ghosh, S., Banacore, A., Norder, P., Bjelcic, M., Kabbinale, A., Nileshwar, P., Wehlander, G., de Sanctis, D., Basu, S., Orlans, J., Vallejos, A., Chavas, L.M.G., Neutze, R., Branden, G.

(2026) J Appl Crystallogr 59: 303-315

PubMed: 41959872 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1600576725011513
Primary Citation Related Structures:
9S39, 9TBL, 9UYR, 9VDJ, 9VDX

PubMed Abstract:
Fixed-target platforms provide convenient support for microcrystals during serial X-ray crystallography studies using synchrotron radiation. Here, we describe a simple user-friendly 3D-printed support where the crystals are sandwiched between two layers of thin X-ray-transparent membrane resulting in very low scattering background. The platform is compatible with magnetic mounting onto the standard goniometer of macromolecular crystallography beamlines. Our design utilizes a 96-well frame that facilitates hanging-drop experiments directly on the membrane using conventional crystallization plates, thereby eliminating multiple pipetting and crystal handling steps. Crystals can be enclosed in a sandwich and packed into 'cassettes', preventing the risk of the sample drying out during room-temperature transportation to synchrotron sources. The versatility of the platform is demonstrated by five structures solved using different crystallization and data-collection strategies. Lysozyme single-crystal rotational crystallography at room temperature is shown, as well as microcrystal serial data collection under cryogenic conditions. On-chip microcrystallization is illustrated by use of a photosynthetic reaction center as an example. Finally, serial crystallography data collection at room temperature from microcrystals of the membrane protein cytochrome c oxidase crystallized in lipidic cubic phase is presented.

Organizational Affiliation

Department of Chemistry and Molecular Biology Gothenburg University Sweden.

Macromolecule Content

Total Structure Weight: 14.67 kDa
Atom Count: 1,121
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 Gene Names: LYZ 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
NA (Subject of Investigation/LOI) Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]