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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 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

PubMed: 29619195 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/c7sc00758b
Primary Citation 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.

Organizational Affiliation

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

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6QGE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	H [auth A], S [auth C], V [auth D]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain S [auth C] Focus chain V [auth D]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth D]	I [auth A], J [auth A], P [auth B], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-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
Version 2.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations
Version 3.0: 2026-08-26
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Non-polymer description, Structure summary