5MF2 | pdb_00005mf2

Bacteriophage T5 distal tail protein pb9 co-crystallized with Tb-Xo4

• PDB DOI: https://doi.org/10.2210/pdb5MF2/pdb

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


• Deposited: 2016-11-17 Released: 2017-09-20 
• Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Lassalle, L., Arnaud, C.-A., Breyton, C., Madern, D., Coquelle, N., Maury, O., Girard, E.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence.

Engilberge, S., Riobe, F., Di Pietro, S., Lassalle, L., Coquelle, N., Arnaud, C.A., Pitrat, D., Mulatier, J.C., Madern, D., Breyton, C., Maury, O., Girard, E.

(2017) Chem Sci 8: 5909-5917

• PubMed: 29619195 
• DOI: https://doi.org/10.1039/c7sc00758b
• Primary Citation of Related Structures:  
  5MF2


• PubMed Abstract: 
  

  Macromolecular crystallography suffers from two major issues: getting well-diffracting crystals and solving the phase problem inherent to large macromolecules. Here, we describe the first example of a lanthanide complex family named "crystallophore" (Xo4), which contributes to tackling both bottlenecks. This terbium complex, Tb-Xo4, is an appealing agent for biocrystallography, combining the exceptional phasing power of the Tb(iii) heavy atom with powerful nucleating properties, providing ready-to-use crystals for structure determination. Furthermore, protein/Tb-Xo4 co-crystals can be easily detected and discriminated from other crystalline by-products using luminescence. We demonstrate the potential of this additive for the crystallisation and structure determination of eight proteins, two of whose structures were unknown.

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Organizational Affiliation: 

Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France . Email: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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: 101.64 kDa 
• Atom Count: 6,196 
• Modeled Residue Count: 732 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7MT	H [auth A], S [auth C], V [auth D]	Tb-Xo4 C20 H23 N5 O4 Tb JWLMJALAUZUFRC-UHFFFAOYSA-L
TB	E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], T [auth D], U [auth D]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
CL	I [auth A], J [auth A], P [auth B], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.464	α = 90
b = 95.502	β = 103.46
c = 71.492	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Lassalle, L., Arnaud, C.-A., Breyton, C., Madern, D., Coquelle, N., Maury, O., Girard, E.

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

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 2.0: 2018-07-25
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-05-29
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.2: 2019-10-16
  Changes: Data collection
• Version 2.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations