5MF2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

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

  • DOI: 10.1039/c7sc00758b

  • 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" ...

    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.


    Related Citations: 
    • Crystal structure of pb9, the distal tail protein of bacteriophage T5: a conserved structural motif among all siphophages.
      Flayhan, A.,Vellieux, F.M.,Lurz, R.,Maury, O.,Contreras-Martel, C.,Girard, E.,Boulanger, P.,Breyton, C.
      (2014) J. Virol. 88: 820


    Organizational Affiliation

    Univ Lyon , Ens de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F-69342 Lyon , France . Email: olivier.maury@ens-lyon.fr.,Univ. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France . Email: eric.girard@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Distal tail protein
A, B, C, D
217Escherichia phage T5Mutation(s): 0 
Gene Names: D16
Find proteins for Q6QGE8 (Escherichia phage T5)
Go to UniProtKB:  Q6QGE8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download SDF File 
Download CCD File 
A, B, C, D
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
7MT
Query on 7MT

Download SDF File 
Download CCD File 
A, C, D
Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.464α = 90.00
b = 95.502β = 103.46
c = 71.492γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
XDSdata reduction
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BS07-0007-01

Revision History 

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