9SQT | pdb_00009sqt

Joint X-ray/neutron room temperature structure of perdeuterated LecA lectin in complex with deuterated galactose

PDB DOI: https://doi.org/10.2210/pdb9SQT/pdb

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

Deposited: 2025-09-23 Released: 2025-12-24
Deposition Author(s): Arnaud, T., Gajdos, L., Devos, J.M., Blakeley, M.P., Varrot, A., Imberty, A.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.157 (Depositor), 0.157 (DCC)
R-Value Observed:
0.158 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.278 (Depositor)
R-Value Work:
0.215 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Neutron Crystallography Study of Host-Pathogen Recognition Enhanced by Hydrogen/Deuterium Exchange on Carbohydrates

Arnaud, T., Tatol, C., Devos, J.M., Gajdos, L., Vidal, S., Korsak, M., Varrot, A., Wimmerova, M., Feuillastre, S., Blakeley, M.P., Imberty, A.

(2025) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2025-4w1cj

Macromolecule Content

Total Structure Weight: 103.92 kDa
Atom Count: 8,160
Modeled Residue Count: 968
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I galactophilic lectin	A, B, C, D, E A, B, C, D, E, F, G, H	121	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: lecA, pa1L, PA2570
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097 Go to UniProtKB: Q05097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA (Subject of Investigation/LOI) Query on GLA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.185 (Depositor), 0.185 (DCC)
R-Value Work: 0.157 (Depositor), 0.157 (DCC)
R-Value Observed: 0.158 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.278 (Depositor)
R-Value Work: 0.215 (Depositor)

Diffraction Data: https://doi.org/10.15151/ESRF-DC-2233251465

Diffraction Data: https://doi.org/10.5291/ILL-DATA.8-01-617

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.799	α = 90
b = 106.522	β = 94.634
c = 83.303	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	22-EXES-0001
Agence Nationale de la Recherche (ANR)	France	ANR-15-IDEX-02
Agence Nationale de la Recherche (ANR)	France	ANR-21-ESRE-0011