Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.09 kDa 
• Atom Count: 1152 
• Residue Count: 129 
• Unique protein chains: 1

5NJR

Mix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 50s time-delay, phased with 4ET8

• DOI: 10.2210/pdb5NJR/pdb

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


• Deposited: 2017-03-29 Released: 2017-10-18 
• Deposition Author(s): Oberthuer, D., Meents, A., Beyerlein, K.R., Chapman, H.N., Lieseke, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5NJS

Literature

Mix-and-diffuse serial synchrotron crystallography.

Beyerlein, K.R., Dierksmeyer, D., Mariani, V., Kuhn, M., Sarrou, I., Ottaviano, A., Awel, S., Knoska, J., Fuglerud, S., Jonsson, O., Stern, S., Wiedorn, M.O., Yefanov, O., Adriano, L., Bean, R., Burkhardt, A., Fischer, P., Heymann, M., Horke, D.A., Jungnickel, K.E.J., Kovaleva, E., Lorbeer, O., Metz, M., Meyer, J., Morgan, A., Pande, K., Panneerselvam, S., Seuring, C., Tolstikova, A., Lieske, J., Aplin, S., Roessle, M., White, T.A., Chapman, H.N., Meents, A., Oberthuer, D.

(2017) IUCrJ 4: 769-777

• PubMed: 29123679 
• DOI: 10.1107/S2052252517013124
• Primary Citation of Related Structures:  
  5NJP, 5NJR, 5NJQ, 5NJS


• PubMed Abstract: 
  

Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.

---

Organizational Affiliation: 

Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.

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
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	B	triacetyl-beta-chitotriose	Oligosaccharide /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.61	α = 90
b = 79.61	β = 90
c = 38.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-29 
• Released Date: 2017-10-18 
Deposition Author(s): Oberthuer, D., Meents, A., Beyerlein, K.R., Chapman, H.N., Lieseke, J.

Revision History 

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary