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: D16, ORF128, T5.139, T5p135
UniProt
Find proteins for Q6QGE8 (Escherichia phage T5)
Explore Q6QGE8 
Go to UniProtKB:  Q6QGE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6QGE8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MT
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],
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 


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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