6TVY

Structure of hen egg white lysozyme crystallized in the presence of Tb-Xo4 crystallophore in the XtalController device

• PDB DOI: https://doi.org/10.2210/pdb6TVY/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2020-01-10 Released: 2020-12-16 
• Deposition Author(s): de Wijn, R., Rollet, K., Coudray, L., McEwen, A.G., Lorber, B., Sauter, C.
• Funding Organization(s): French National Research Agency, French Infrastructure for Integrated Structural Biology (FRISBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.175 
• R-Value Work: 0.141 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering

de Wijn, R., Rollet, K., Engilberge, S., McEwen, A.G., Hennig, O., Betat, H., Moerl, M., Riobe, F., Maury, O., Girard, E., Benas, P., Lorber, B., Sauter, C.

(2020) Crystals (Basel) 

• DOI: https://doi.org/10.3390/cryst10020065

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: light scattering, gel filtration

Macromolecule Content

• Total Structure Weight: 15.3 kDa 
• Atom Count: 1,090 
• 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MT (Subject of Investigation/LOI)	E [auth A]	Tb-Xo4 C20 H23 N5 O4 Tb JWLMJALAUZUFRC-UHFFFAOYSA-L
TB	F [auth A], G [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.175 
• R-Value Work: 0.141 
• R-Value Observed: 0.145 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.81	α = 90
b = 78.81	β = 90
c = 38.332	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): de Wijn, R., Rollet, K., Coudray, L., McEwen, A.G., Lorber, B., Sauter, C.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-LABX-0036_NETRNA
French National Research Agency	France	ANR-11-LABX-0057_MITOCROSS
French National Research Agency	France	ANR-10-LABX-0036_INRT
French National Research Agency	France	ANR-13-BS07-0007-01
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INSB-05

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary