6JZI | pdb_00006jzi

Structure of hen egg-white lysozyme obtained from SFX experiments under atmospheric pressure

• PDB DOI: https://doi.org/10.2210/pdb6JZI/pdb

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


• Deposited: 2019-05-02 Released: 2019-10-30 
• Deposition Author(s): Nango, E., Sugahara, M., Nakane, T., Tanaka, T., Iwata, S.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.

Shimazu, Y., Tono, K., Tanaka, T., Yamanaka, Y., Nakane, T., Mori, C., Terakado Kimura, K., Fujiwara, T., Sugahara, M., Tanaka, R., Doak, R.B., Shimamura, T., Iwata, S., Nango, E., Yabashi, M.

(2019) J Appl Crystallogr 52: 1280-1288

• PubMed: 31798359 
• DOI: https://doi.org/10.1107/S1600576719012846
• Primary Citation Related Structures: 
  6JZH, 6JZI


• PubMed Abstract: 
  

  A sample-injection device has been developed at SPring-8 Angstrom Compact Free-Electron Laser (SACLA) for serial femtosecond crystallography (SFX) at atmospheric pressure. Microcrystals embedded in a highly viscous carrier are stably delivered from a capillary nozzle with the aid of a coaxial gas flow and a suction device. The cartridge-type sample reservoir is easily replaceable and facilitates sample reloading or exchange. The reservoir is positioned in a cooling jacket with a temperature-regulated water flow, which is useful to prevent drastic changes in the sample temperature during data collection. This work demonstrates that the injector successfully worked in SFX of the human A _2A adenosine receptor complexed with an antagonist, ZM241385, in lipidic cubic phase and for hen egg-white lysozyme microcrystals in a grease carrier. The injection device has also been applied to many kinds of proteins, not only for static structural analyses but also for dynamics studies using pump-probe techniques.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 14.43 kDa 
• Atom Count: 1,089 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1572698

Diffraction Data: https://doi.org/10.11577/1572697

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.11	α = 90
b = 79.11	β = 90
c = 38.02	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Nango, E., Sugahara, M., Nakane, T., Tanaka, T., Iwata, S.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	X-ray Free-Electron Laser Priority Strategy Program

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-22
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary