8P1D | pdb_00008p1d

Lysozyme structure solved from serial crystallography data collected at 100 Hz with JUNGFRAU detector at MAXIV

• PDB DOI: https://doi.org/10.2210/pdb8P1D/pdb

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


• Deposited: 2023-05-11 Released: 2023-10-18 
• Deposition Author(s): Nan, J., Leonarski, F., Furrer, A., Dworkowski, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source.

Leonarski, F., Nan, J., Matej, Z., Bertrand, Q., Furrer, A., Gorgisyan, I., Bjelcic, M., Kepa, M., Glover, H., Hinger, V., Eriksson, T., Cehovin, A., Eguiraun, M., Gasparotto, P., Mozzanica, A., Weinert, T., Gonzalez, A., Standfuss, J., Wang, M., Ursby, T., Dworkowski, F.

(2023) IUCrJ 10: 729-737

• PubMed: 37830774 
• DOI: https://doi.org/10.1107/S2052252523008618
• Primary Citation Related Structures: 
  8P1A, 8P1B, 8P1C, 8P1D


• PubMed Abstract: 
  

  Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously. A high-quality complete X-ray dataset was obtained within 1 min from lysozyme microcrystals, and the dynamics of the light-driven sodium-pump membrane protein KR2 with a time resolution of 1 ms could be demonstrated. To make the setup more accessible for researchers, downstream data handling and analysis will be automated to allow on-the-fly spot finding and indexing, as well as data processing.

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Organizational Affiliation: 
• Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland.
MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden.
Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland.
Scientific Computing, Theory and Data, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland.

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: 14.55 kDa 
• Atom Count: 1,146 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.48391/b0c36bb8-a00c-4519-8dcc-08d5ca60a313

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.06	α = 90
b = 79.06	β = 90
c = 38.26	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: 2023-10-18 
Deposition Author(s): Nan, J., Leonarski, F., Furrer, A., Dworkowski, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Database references
• Version 1.2: 2023-11-15
  Changes: Database references
• Version 1.3: 2024-11-13
  Changes: Structure summary