8CL5 | pdb_00008cl5

Lysozyme in matrix of lipidic cubic phase of monoolein (LCP)

• PDB DOI: https://doi.org/10.2210/pdb8CL5/pdb

• Classification: HYDROLASE
• Organism(s): Asplenium bulbiferum subsp. bulbiferum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-16 Released: 2023-12-13 
• Deposition Author(s): Bertrand, Q., Kepa, M.W., Weinert, T., Wranik, M., Standfuss, J.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.

Wranik, M., Kepa, M.W., Beale, E.V., James, D., Bertrand, Q., Weinert, T., Furrer, A., Glover, H., Gashi, D., Carrillo, M., Kondo, Y., Stipp, R.T., Khusainov, G., Nass, K., Ozerov, D., Cirelli, C., Johnson, P.J.M., Dworkowski, F., Beale, J.H., Stubbs, S., Zamofing, T., Schneider, M., Krauskopf, K., Gao, L., Thorn-Seshold, O., Bostedt, C., Bacellar, C., Steinmetz, M.O., Milne, C., Standfuss, J.

(2023) Nat Commun 14: 7956-7956

• PubMed: 38042952 
• DOI: https://doi.org/10.1038/s41467-023-43523-5
• Primary Citation Related Structures: 
  8CL5, 8CL6, 8CL7, 8CL8, 8CL9, 8CLB, 8CLC, 8CLD, 8CLE, 8CLF, 8CLG, 8CLH


• PubMed Abstract: 
  

  Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.

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Organizational Affiliation: 
• Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland. [e-mail].
Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland. [e-mail].
Laboratory for Synchrotron Radiation and Femtochemistry, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen-PSI, Villigen, 5232, Switzerland.
Laboratory of Nanoscale Biology, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Scientific Computing, Theory and Data Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Laboratory for Nonlinear Optics, Photon Science Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Large Research Facilities Division, Paul Scherrer Institut, Villigen-PSI, 5232, Villigen, Switzerland.
Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, Munich, 81377, Germany.
LUXS Laboratory for Ultrafast X-ray Sciences, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
Biozentrum, University of Basel, 4056, Basel, Switzerland.
Femtosecond X-ray Experiments Instrument, European XFEL GmbH, Schenefeld, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.75 kDa 
• Atom Count: 1,329 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME, Chain A	A	129	Asplenium bulbiferum subsp. bulbiferum	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.92	α = 90
b = 77.92	β = 90
c = 37.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Bertrand, Q., Kepa, M.W., Weinert, T., Wranik, M., Standfuss, J.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_179351
Swiss National Science Foundation	Switzerland	310030_207462
Swiss National Science Foundation	Switzerland	310030_192566

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary