5MJJ | pdb_00005mjj

Single-shot pink beam serial crystallography: Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb5MJJ/pdb

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


• Deposited: 2016-12-01 Released: 2017-12-20 
• Deposition Author(s): Meents, A., Oberthuer, D., Lieske, J., Srajer, V.
• Funding Organization(s): European Cluster of Advanced Laser Light Sources (EUCALL, Virtual Institute VH-VI-403, Helmholtz Association, Advanced Photon Source, a U.S. Department of Energy (DOE), Argonne National Laboratory, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Philip Anfinrud (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Single-shot pink beam serial crystallography: Lysozyme

Meents, A., Oberthuer, D., Lieske, J., Srajer, V.

To be published.

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: 14.39 kDa 
• Atom Count: 1,196 
• 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  Gene Names: LYZ 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 37.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Precognition/Epinorm (RenzResearch)	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Meents, A., Oberthuer, D., Lieske, J., Srajer, V.

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Funding Organization	Location	Grant Number
European Cluster of Advanced Laser Light Sources (EUCALL		--
Virtual Institute VH-VI-403, Helmholtz Association		--
Advanced Photon Source, a U.S. Department of Energy (DOE), Argonne National Laboratory		DE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		R24GM111072
Philip Anfinrud (NIH/NIDDK)		NSF award 1231306

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2022-03-30
  Changes: Author supporting evidence, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary