8CWC

20ns Temperature-Jump (Light) XFEL structure of Lysozyme Bound to N,N'-diacetylchitobiose

• PDB DOI: https://doi.org/10.2210/pdb8CWC/pdb

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


• Deposited: 2022-05-19 Released: 2022-06-22 
• Deposition Author(s): Wolff, A.M., Thompson, M.C., Fraser, J.S., Nango, E.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.169 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 

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: 14.98 kDa 
• Atom Count: 1,155 
• 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05026ZL GlyCosmos:  G05026ZL GlyGen:  G05026ZL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.169 
• R-Value Work: 0.132 
• R-Value Observed: 0.134 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.11577/1873469

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.061	α = 90
b = 77.061	β = 90
c = 37.223	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
cxi.merge	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Wolff, A.M., Thompson, M.C., Fraser, J.S., Nango, E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 2.0: 2023-01-25
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references
• Version 2.2: 2023-10-04
  Changes: Database references
• Version 2.3: 2023-10-25
  Changes: Refinement description
• Version 2.4: 2023-11-15
  Changes: Database references