6F2K | pdb_00006f2k

Crystal structure of Hen Egg-White Lysozyme co-crystallized in presence of 100 mM Tb-Xo4 and 100 mM potassium phosphate monobasic.

• PDB DOI: https://doi.org/10.2210/pdb6F2K/pdb

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


• Deposited: 2017-11-24 Released: 2018-10-03 
• Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Girard, E., Dumont, E., Maury, O.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.

Engilberge, S., Riobe, F., Wagner, T., Di Pietro, S., Breyton, C., Franzetti, B., Shima, S., Girard, E., Dumont, E., Maury, O.

(2018) Chemistry 24: 9739-9746

• PubMed: 29806881 
• DOI: https://doi.org/10.1002/chem.201802172
• Primary Citation Related Structures: 
  6F2F, 6F2H, 6F2I, 6F2J, 6F2K, 6F2M, 6FRM, 6FRN, 6FRO, 6FRQ


• PubMed Abstract: 
  

  Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4). Such interaction mapping analyses demonstrate the versatile binding behavior of the Crystallophore and pave the way to a better understanding of its unique properties.

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Organizational Affiliation: 
• Univ Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.
Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 518, F-69342, Lyon, France.
Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, 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: 14.6 kDa 
• Atom Count: 1,215 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB	B [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.240 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.359	α = 90
b = 78.359	β = 90
c = 37.404	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Girard, E., Dumont, E., Maury, O.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-BS07-0007-01

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary