6RNB | pdb_00006rnb

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Lysozyme with GlcNAc3 50ms diffusion time

• PDB DOI: https://doi.org/10.2210/pdb6RNB/pdb

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


• Deposited: 2019-05-08 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: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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 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.
Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany.
Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen Synchrotron, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Scientific Support Unit Machine Physics, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany. [e-mail].
Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany. [e-mail].
University of Toronto, Departments of Chemistry and Physics, Toronto, Ontario, Canada. [e-mail].

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: 15.05 kDa 
• Atom Count: 1,126 
• 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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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

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	E [auth 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:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 78.7	β = 90
c = 37.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	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: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary