8H8U

Room-temperature structure of lysozyme by pink-beam serial crystallography (50 ms, center)

• PDB DOI: https://doi.org/10.2210/pdb8H8U/pdb

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


• Deposited: 2022-10-24 Released: 2023-11-01 
• Deposition Author(s): Kim, Y., Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Data of pink-beam serial synchrotron crystallography at the Pohang Light Source II.

Kim, Y., Nam, K.H.

(2024) Data Brief 52: 109811-109811

• PubMed: 38161663 
• DOI: https://doi.org/10.1016/j.dib.2023.109811
• Primary Citation of Related Structures:  
  8H8T, 8H8U, 8H8V, 8H8W


• PubMed Abstract: 
  

  Serial synchrotron crystallography (SSX) helps to determine the room-temperature structure of macromolecules with minimal radiation damage. Pink-beam X-ray provides more photon flux than a monochromatic beam, which can increase the diffraction intensity of crystal samples and reduce the issue of partial reflection measurement compared with a monochromatic beam. The demonstration of pink-beam SSX at the 1C beamline at the Pohang Light Source II (PLS-II) was previously reported. The Bragg peaks observed in SSX diffraction data using a pink-beam exhibited a slightly stretched shape, unlike that from a monochromatic beam. Therefore, it is necessary to develop an indexing algorithm that can efficiently process the Bragg peak generated by pink-beam SSX. Therefore, the collected pink-beam SSX diffraction data can be tentatively used to develop an indexing program for Bragg peaks generated using the pink-beam. In this study, detailed information on the diffraction data of pink-beam SSX at PLS-II was reported to access the raw data and process the information.

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Organizational Affiliation: 

Pohang Accelerator Laboratory, Pohang University of Science and Technology, 37673, Republic of Korea.

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: 14.43 kDa 
• Atom Count: 1,121 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.88	α = 90
b = 78.88	β = 90
c = 38.05	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Kim, Y., Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020M3H1A1075314
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary