5MF2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


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
  • 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 ...

    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. Grenoble Alpes , CEA , CNRS , IBS , F-38000 Grenoble , France . Email: eric.girard@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Distal tail proteinA, B, C, D217Escherichia virus T5Mutation(s): 0 
Gene Names: D16ORF128T5.139T5p135
UniProt
Find proteins for Q6QGE8 (Escherichia phage T5)
Explore Q6QGE8 
Go to UniProtKB:  Q6QGE8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MT (Subject of Investigation/LOI)
Query on 7MT

Download Ideal Coordinates CCD File 
H [auth A], S [auth C], V [auth D]Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
TB
Query on TB

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], P [auth B], W [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.464α = 90
b = 95.502β = 103.46
c = 71.492γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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