7PRG

Joint X-ray/neutron room temperature structure of perdeuterated LecB lectin in complex with perdeuterated fucose

PDB DOI: https://doi.org/10.2210/pdb7PRG/pdb

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

Deposited: 2021-09-21 Released: 2022-01-12
Deposition Author(s): Gajdos, L., Blakeley, M.P., Haertlein, M., Forsyth, T.V., Devos, J.M., Imberty, A.
Funding Organization(s): Institut Laue-Langevin

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.142
R-Value Work: 0.104
R-Value Observed: 0.106

Method: NEUTRON DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.246
R-Value Work: 0.191
R-Value Observed: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding.

Gajdos, L., Blakeley, M.P., Haertlein, M., Forsyth, V.T., Devos, J.M., Imberty, A.

(2022) Nat Commun 13: 194-194

PubMed: 35017516 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27871-8
Primary Citation of Related Structures:
7PRG, 7PSY

PubMed Abstract:
The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low-barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.

Organizational Affiliation

Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 48.54 kDa
Atom Count: 3,979
Modelled Residue Count: 456
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, B, C, D	115	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070... lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
UniProt
Find proteins for A0A069Q9V4 (Pseudomonas aeruginosa) Explore A0A069Q9V4 Go to UniProtKB: A0A069Q9V4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A069Q9V4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC (Subject of Investigation/LOI) Query on FUC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D]	G [auth A], J [auth B], N [auth C], O [auth D]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth D]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] L [auth C] E [auth A], F [auth A], H [auth B], I [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.142
R-Value Work: 0.104
R-Value Observed: 0.106
Space Group: P 1 2₁ 1

Method: NEUTRON DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.246
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.9	α = 90
b = 73.87	β = 94.58
c = 55.003	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Coot	model building
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Institut Laue-Langevin	France	--

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2022-01-26
Changes: Database references
Version 1.2: 2024-05-01
Changes: Data collection, Experimental preparation, Refinement description