6F2M

Structure of the bacteriophage T5 distal tail protein pb9 co-crystallized with 10mM Tb-Xo4

• PDB DOI: https://doi.org/10.2210/pdb6F2M/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Tequintavirus T5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-24 Released: 2018-10-03 
• Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Breyton, C., 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: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

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 of 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.15 kDa 
• Atom Count: 6,520 
• Modelled Residue Count: 727 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Distal tail protein	A, B, C, D	217	Tequintavirus T5	Mutation(s): 0  Gene Names: D16, ORF128, T5.139, T5p135
UniProt
Find proteins for Q6QGE8 (Escherichia phage T5) Explore Q6QGE8  Go to UniProtKB:  Q6QGE8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MT	E [auth A], K [auth C], N [auth D]	Tb-Xo4 C20 H23 N5 O4 Tb JWLMJALAUZUFRC-UHFFFAOYSA-L
TB	J [auth B], M [auth D]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], L [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.4	α = 90
b = 95.24	β = 102.66
c = 71.584	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Breyton, C., 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: 2019-05-29
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations