PDB-9g3l: LecB from PA01 in complex with synthetic beta - fucosylamide

ID or keywords:

Entry

Database: PDB / ID: 9g3l

Title

LecB from PA01 in complex with synthetic beta - fucosylamide

Components

Fucose-binding lectin PA-IIL

Keywords

SUGAR BINDING PROTEIN / Lectin / beta-fucosylamide / anti-adhesive / Pseudomonas

Function / homology

Function and homology information

single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.739 Å

Authors

Antonini, G. / Varrot, A.

Funding support

European Union, 1items

Citation

Journal: J.Med.Chem. / Year: 2025
Title: Toward Dual-Target Glycomimetics against Two Bacterial Lectins to Fight Pseudomonas aeruginosa - Burkholderia cenocepacia Infections: A Biophysical Study.
Authors: Antonini, G. / Fares, M. / Hauck, D. / Mala, P. / Gillon, E. / Belvisi, L. / Bernardi, A. / Titz, A. / Varrot, A. / Mazzotta, S.

History

Deposition	Jul 12, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2025	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	May 21, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9g3l.cif.gz	118.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9g3l.ent.gz		Display	PDB format
PDBx/mmJSON format	9g3l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9g3l_validation.pdf.gz	5.4 MB	Display	wwPDB validaton report
Full document	9g3l_full_validation.pdf.gz	5.4 MB	Display
Data in XML	9g3l_validation.xml.gz	29.1 KB	Display
Data in CIF	9g3l_validation.cif.gz	40.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g3/9g3l ftp://data.pdbj.org/pub/pdb/validation_reports/g3/9g3l	HTTPS FTP

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Related structure data

Related structure data	9g3kC 9h0qC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.12794355 / Data set type: diffraction image data Details: X-ray diffraction data set for PDB 9G3L: LecB from PA01 in complex with beta-fucosylamide-indole derivative Metadata reference: 10.5281/zenodo.12794355

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fucose-binding lectin PA-IIL

B: Fucose-binding lectin PA-IIL

C: Fucose-binding lectin PA-IIL

D: Fucose-binding lectin PA-IIL

hetero molecules

48.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.019, 80.160, 52.429
Angle α, β, γ (deg.)	90.000, 109.607, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Fucose-binding lectin PA-IIL Mass: 11734.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lecB, PA3361 / Plasmid: PET25B-LecB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYN5
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-R7E / 5-[3-(aminomethyl)phenyl]-~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]furan-2-carboxamide / (5-(3'-aminomethyl)phenyl)furan-2-carboxamido-b-L-fucopyranose Mass: 362.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar	ChemComp-A1IH4 / beta-L-fucopyranosyl-1H-indole-6-carboxamide / N-[(2S,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]-1H-indole-5-carboxamide Type: L-saccharide, beta linking / Mass: 306.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₅H₁₈N₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.03 Å³/Da / Density % sol: 69.53 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 26% Peg6K 1M LiCl 0.1M sodium acetate pH 4.5 3 minutes soaking in 32% Peg Smear Low 50 mM sodium acetate pH 4.5 and 10mM ligand

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 1.739→49.39 Å / Num. obs: 40572 / % possible obs: 99.2 % / Redundancy: 5.2 % / CC_1/2: 0.994 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.099 / R_rim(I) all: 0.172 / Net I/σ(I): 7.6
Reflection shell	Resolution: 1.74→1.77 Å / R_merge(I) obs: 0.815 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1952 / CC_1/2: 0.678 / R_pim(I) all: 0.584

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.739→49.389 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / SU B: 2.545 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1878	2073	5.113 %
R_work	0.1474	38474	-
all	0.15	-	-
obs	-	40572	99.127 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 11.841 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.138 Å²	0 Å²	-0.388 Å²
2-	-	2.412 Å²	0 Å²
3-	-	-	-1.593 Å²

Refinement step

Cycle: LAST / Resolution: 1.739→49.389 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3308	0	100	551	3959

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	3473
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3189
X-RAY DIFFRACTION	r_angle_refined_deg	1.692	1.771	4777
X-RAY DIFFRACTION	r_angle_other_deg	0.638	1.723	7271
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.862	5	458
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.741	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.623	10	475
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.585	10	153
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	597
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4257
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	823
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	593
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	2800
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1774
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	1935
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	415
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.196	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.069	0.2	30
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.187	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.255	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	57
X-RAY DIFFRACTION	r_mcbond_it	1.33	1.149	1835
X-RAY DIFFRACTION	r_mcbond_other	1.33	1.148	1834
X-RAY DIFFRACTION	r_mcangle_it	1.769	2.055	2292
X-RAY DIFFRACTION	r_mcangle_other	1.768	2.056	2293
X-RAY DIFFRACTION	r_scbond_it	2.38	1.376	1638
X-RAY DIFFRACTION	r_scbond_other	2.379	1.376	1639
X-RAY DIFFRACTION	r_scangle_it	3.46	2.426	2485
X-RAY DIFFRACTION	r_scangle_other	3.46	2.427	2486
X-RAY DIFFRACTION	r_lrange_it	4.902	17.833	4010
X-RAY DIFFRACTION	r_lrange_other	4.376	16.035	3818
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.1	0.05	3372
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.09	0.05	3394
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.088	0.05	3378
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	3348
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.094	0.05	3326
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.095	0.05	3382

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09994	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09994	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09019	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09019	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08832	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.08832	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09287	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.09287	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09436	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.09436	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09498	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09498	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.739-1.784	0.318	112	0.271	2612	X-RAY DIFFRACTION	90.4382
1.784-1.833	0.287	141	0.242	2785	X-RAY DIFFRACTION	99.5916
1.833-1.886	0.233	132	0.209	2714	X-RAY DIFFRACTION	99.7197
1.886-1.944	0.206	142	0.173	2615	X-RAY DIFFRACTION	99.7107
1.944-2.007	0.225	165	0.156	2516	X-RAY DIFFRACTION	99.7767
2.007-2.078	0.189	142	0.153	2453	X-RAY DIFFRACTION	99.8077
2.078-2.156	0.167	125	0.128	2367	X-RAY DIFFRACTION	99.9198
2.156-2.244	0.172	97	0.12	2310	X-RAY DIFFRACTION	99.917
2.244-2.343	0.183	114	0.122	2209	X-RAY DIFFRACTION	100
2.343-2.458	0.156	123	0.114	2096	X-RAY DIFFRACTION	100
2.458-2.59	0.157	127	0.111	1987	X-RAY DIFFRACTION	99.9527
2.59-2.747	0.171	120	0.115	1880	X-RAY DIFFRACTION	99.9001
2.747-2.936	0.167	106	0.121	1774	X-RAY DIFFRACTION	99.9468
2.936-3.17	0.178	108	0.136	1643	X-RAY DIFFRACTION	100
3.17-3.471	0.168	85	0.145	1531	X-RAY DIFFRACTION	100
3.471-3.879	0.182	57	0.134	1400	X-RAY DIFFRACTION	100
3.879-4.474	0.18	60	0.124	1242	X-RAY DIFFRACTION	100
4.474-5.468	0.16	53	0.139	1047	X-RAY DIFFRACTION	100
5.468-7.686	0.258	41	0.223	826	X-RAY DIFFRACTION	100

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