6F7W | pdb_00006f7w

Crystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form

PDB DOI: https://doi.org/10.2210/pdb6F7W/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-12-12 Released: 2018-05-30
Deposition Author(s): Guagnini, F., Rennie, M.L., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.151 (Depositor), 0.151 (DCC)
R-Value Work:
0.124 (Depositor), 0.124 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein.

Guagnini, F., Antonik, P.M., Rennie, M.L., O'Byrne, P., Khan, A.R., Pinalli, R., Dalcanale, E., Crowley, P.B.

(2018) Angew Chem Int Ed Engl 57: 7126-7130

PubMed: 29673020 Search on PubMed
DOI: https://doi.org/10.1002/anie.201803232
Primary Citation Related Structures:
6F7W, 6F7X, 6F7Y

PubMed Abstract:
Here, we provide the first structural characterization of host-guest complexation between cucurbit[7]uril (Q7) and dimethyllysine (KMe ₂ ) in a model protein. Binding was dominated by complete encapsulation of the dimethylammonium functional group. While selectivity for the most sterically accessible dimethyllysine was observed both in solution and in the solid state, three different modes of Q7-KMe ₂ complexation were revealed by X-ray crystallography. The crystal structures revealed also entrapped water molecules that solvated the ammonium group within the Q7 cavity. Remarkable Q7-protein assemblies, including inter-locked octahedral cages that comprise 24 protein trimers, occurred in the solid state. Cucurbituril clusters appear to be responsible for these assemblies, suggesting a strategy to generate controlled protein architectures.

Organizational Affiliation

School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.

Macromolecule Content

Total Structure Weight: 33.78 kDa
Atom Count: 2,792
Modeled Residue Count: 268
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C	90	Ralstonia solanacearum	Mutation(s): 0 Gene Names: RSP795_21825, RSP799_05830, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QQ7 (Subject of Investigation/LOI) Query on QQ7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C]	D [auth A], H [auth B], L [auth C]	cucurbit[7]uril C₄₂ H₄₂ N₂₈ O₁₄ ZDOBFUIMGBWEAB-XGFHMVPTSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.151 (Depositor), 0.151 (DCC)
R-Value Work: 0.124 (Depositor), 0.124 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.343	α = 90
b = 87.176	β = 90
c = 146.595	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Guagnini, F.

Rennie, M.L.

Crowley, P.B.

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/ERC/B2912 and 13/CDA/2168

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2018-06-13
Changes: Data collection, Database references
Version 2.0: 2020-08-05
Changes: Data collection, Derived calculations, Polymer sequence
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description