6F2M | pdb_00006f2m

Structure of the bacteriophage T5 distal tail protein pb9 co-crystallized with 10mM Tb-Xo4

PDB DOI: https://doi.org/10.2210/pdb6F2M/pdb

Classification: VIRAL PROTEIN
Organism(s): Tequintavirus T5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-24 Released: 2018-10-03
Deposition Author(s): Engilberge, S., Riobe, F., Di Pietro, S., Breyton, C., Girard, E., Dumont, E., Maury, O.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor), 0.201 (DCC)
R-Value Work:
0.178 (Depositor), 0.181 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.

Engilberge, S., Riobe, F., Wagner, T., Di Pietro, S., Breyton, C., Franzetti, B., Shima, S., Girard, E., Dumont, E., Maury, O.

(2018) Chemistry 24: 9739-9746

PubMed: 29806881 Search on PubMed
DOI: https://doi.org/10.1002/chem.201802172
Primary Citation Related Structures:
6F2F, 6F2H, 6F2I, 6F2J, 6F2K, 6F2M, 6FRM, 6FRN, 6FRO, 6FRQ

PubMed Abstract:
Crystallophores are lanthanide complexes that act as powerful auxiliary for protein crystallography due to their strong nucleating and phasing effects. To get first insights on the mechanisms behind nucleation induced by Crystallophore, we systematically identified various elaborated networks of supramolecular interactions between Tb-Xo4 and subset of 6 protein structures determined by X-ray diffraction in complex with terbium-Crystallophore (Tb-Xo4). Such interaction mapping analyses demonstrate the versatile binding behavior of the Crystallophore and pave the way to a better understanding of its unique properties.

Organizational Affiliation

Univ Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 100.15 kDa
Atom Count: 6,520
Modeled Residue Count: 727
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7MT Query on 7MT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], K [auth C], N [auth D]	Tb-Xo4 C₂₀ H₂₃ N₅ O₄ Tb JWLMJALAUZUFRC-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth C] Focus chain N [auth D]
TB Query on TB Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D]	J [auth B], M [auth D]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth D] Interactions & Density Focus chain J [auth B] Focus chain M [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C]	F [auth A], G [auth A], L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203 (Depositor), 0.201 (DCC)
R-Value Work: 0.178 (Depositor), 0.181 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.4	α = 90
b = 95.24	β = 102.66
c = 71.584	γ = 90

Software Package:

Software Name	Purpose
BUSTER	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: 2018-10-03

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: 2018-10-03
Type: Initial release
Version 1.1: 2019-05-29
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations