6QNB

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Lysozyme with GlcNAc3

• PDB DOI: https://doi.org/10.2210/pdb6QNB/pdb

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


• Deposited: 2019-02-10 Released: 2019-10-02 
• Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Liquid application method for time-resolved analyses by serial synchrotron crystallography.

Mehrabi, P., Schulz, E.C., Agthe, M., Horrell, S., Bourenkov, G., von Stetten, D., Leimkohl, J.P., Schikora, H., Schneider, T.R., Pearson, A.R., Tellkamp, F., Miller, R.J.D.

(2019) Nat Methods 16: 979-982

• PubMed: 31527838 
• DOI: https://doi.org/10.1038/s41592-019-0553-1
• Primary Citation of Related Structures:  
  6QNB, 6QNC, 6QND, 6QNH, 6QNI, 6QNJ, 6RNB, 6RNC, 6RND, 6RNF


• PubMed Abstract: 
  

  We introduce a liquid application method for time-resolved analyses (LAMA), an in situ mixing approach for serial crystallography. Picoliter-sized droplets are shot onto chip-mounted protein crystals, achieving near-full ligand occupancy within theoretical diffusion times. We demonstrate proof-of-principle binding of GlcNac to lysozyme, and resolve glucose binding and subsequent ring opening in a time-resolved study of xylose isomerase.

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Organizational Affiliation: 

Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, 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: 14.96 kDa 
• Atom Count: 1,147 
• 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  Gene Names: LYZ 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-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

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: 0.211 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.21	α = 90
b = 79.21	β = 90
c = 38.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary