PDB-8aiy: STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN P...

ID or keywords:

Entry

Database: PDB / ID: 8aiy

Title

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide (4i)

Components

Fucose-binding lectin PA-IIL

Keywords

SUGAR BINDING PROTEIN / P. aeruginosa lectin / LecB / Inhibitor

Function / homology

Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / single-species biofilm formation / carbohydrate binding / metal ion binding / N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide / Fucose-binding lectin PA-IIL

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Meiers, J. / Mala, P. / Varrot, A. / Siebs, E. / Imberty, A. / Titz, A.

Funding support

France, 1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Discovery of N -beta-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB.
Authors: Mala, P. / Siebs, E. / Meiers, J. / Rox, K. / Varrot, A. / Imberty, A. / Titz, A.

History

Deposition	Jul 27, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2022	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
Revision 1.2	Dec 21, 2022	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8aiy.cif.gz	120.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8aiy.ent.gz		Display	PDB format
PDBx/mmJSON format	8aiy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8aiy_validation.pdf.gz	648.2 KB	Display	wwPDB validaton report
Full document	8aiy_full_validation.pdf.gz	649.4 KB	Display
Data in XML	8aiy_validation.xml.gz	9.9 KB	Display
Data in CIF	8aiy_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ai/8aiy ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8aiy	HTTPS FTP

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Related structure data

Related structure data	8aijC 5a3oS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Fucose-binding lectin PA-IIL

BBB: Fucose-binding lectin PA-IIL

CCC: Fucose-binding lectin PA-IIL

DDD: Fucose-binding lectin PA-IIL

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, P. aeruginosa LecB has been intensively described by literature, e.g. by Imberty et al., Gilboa-Carter et al., Titz et al..

Unit cell

Length a, b, c (Å)	71.909, 76.495, 184.306
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	AAA-398- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

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

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	2	1	BBB	B
3	3	2	AAA	A
4	4	2	CCC	C
5	5	3	AAA	A
6	6	3	DDD	D
7	7	4	BBB	B
8	8	4	CCC	C
9	9	5	BBB	B
10	10	5	DDD	D
11	11	6	CCC	C
12	12	6	DDD	D

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) / Gene: lecB, PA3361 / 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
#3: Chemical	ChemComp-MJO / N-(beta-L-Fucopyranosyl)-biphenyl-3-carboxamide / ~{N}-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]-3-phenyl-benzamide Mass: 343.374 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₁₉H₂₁NO₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.44 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 28% PEG 8K, 200 mM (NH4)2SO4, 100 mM tris

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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: 0.97856 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2021
Radiation	Monochromator: channel cut cryogenically cooled monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.55→46.08 Å / Num. obs: 711298 / % possible obs: 99.97 % / Redundancy: 2 % / B_iso Wilson estimate: 18.9 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.041 / R_rim(I) all: 0.092 / Net I/σ(I): 13.57
Reflection shell	Resolution: 1.55→1.58 Å / R_merge(I) obs: 0.557 / Mean I/σ(I) obs: 3.43 / Num. unique obs: 36020 / CC_1/2: 0.902 / R_pim(I) all: 0.272 / R_rim(I) all: 0.092

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5A3O

5a3o

Resolution: 1.55→46.076 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.968 / SU B: 1.095 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1659	3662	4.954 %
R_work	0.1425	70251	-
all	0.144	-	-
obs	-	73913	99.984 %

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: 19.305 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.928 Å²	-0 Å²	-0 Å²
2-	-	-0.373 Å²	0 Å²
3-	-	-	-0.555 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→46.076 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3294	0	118	627	4039

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	3502
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3208
X-RAY DIFFRACTION	r_angle_refined_deg	1.717	1.627	4821
X-RAY DIFFRACTION	r_angle_other_deg	1.577	1.573	7311
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.293	5	466
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.973	25.75	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.677	15	473
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.745	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	500
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4262
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	842
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	628
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	2976
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	1827
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1920
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	446
X-RAY DIFFRACTION	r_metal_ion_refined	0.065	0.2	32
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.098	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.173	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.083	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.368	1.847	1855
X-RAY DIFFRACTION	r_mcbond_other	1.369	1.847	1853
X-RAY DIFFRACTION	r_mcangle_it	1.789	2.768	2324
X-RAY DIFFRACTION	r_mcangle_other	1.789	2.768	2324
X-RAY DIFFRACTION	r_scbond_it	2.405	2.026	1647
X-RAY DIFFRACTION	r_scbond_other	2.385	2.024	1640
X-RAY DIFFRACTION	r_scangle_it	3.375	2.973	2497
X-RAY DIFFRACTION	r_scangle_other	3.367	2.971	2486
X-RAY DIFFRACTION	r_lrange_it	4.575	24.95	4010
X-RAY DIFFRACTION	r_lrange_other	4.247	23.793	3821
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	3327
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.091	0.05	3314
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.084	0.05	3389
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.092	0.05	3327
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.091	0.05	3375
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.091	0.05	3319

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.09868	0.05008
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.09868	0.05008
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.09111	0.05008
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.09111	0.05008
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.0835	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.0835	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.09246	0.05008
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.09246	0.05008
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.09129	0.05008
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.09129	0.05008
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.09098	0.05008
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09098	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.55-1.59	0.199	271	0.177	5148	0.178	5419	0.927	0.935	100	0.164
1.59-1.634	0.196	280	0.167	4972	0.169	5252	0.937	0.943	100	0.154
1.634-1.681	0.192	227	0.155	4891	0.157	5118	0.938	0.953	100	0.143
1.681-1.733	0.177	266	0.147	4709	0.148	4975	0.952	0.961	100	0.135
1.733-1.789	0.172	237	0.138	4595	0.139	4833	0.962	0.967	99.9793	0.126
1.789-1.852	0.175	224	0.137	4460	0.139	4684	0.958	0.967	100	0.127
1.852-1.922	0.184	222	0.139	4297	0.141	4520	0.962	0.966	99.9779	0.131
1.922-2	0.163	217	0.133	4165	0.135	4382	0.967	0.972	100	0.127
2-2.089	0.151	176	0.133	3991	0.133	4167	0.971	0.974	100	0.13
2.089-2.191	0.165	193	0.136	3832	0.138	4025	0.969	0.973	100	0.134
2.191-2.309	0.153	190	0.125	3603	0.127	3793	0.971	0.979	100	0.125
2.309-2.449	0.159	179	0.129	3434	0.131	3613	0.969	0.974	100	0.13
2.449-2.617	0.154	175	0.134	3246	0.135	3421	0.969	0.973	100	0.138
2.617-2.826	0.145	171	0.13	2986	0.131	3157	0.974	0.976	100	0.137
2.826-3.095	0.167	133	0.145	2832	0.146	2965	0.964	0.971	100	0.154
3.095-3.458	0.185	134	0.156	2520	0.158	2654	0.964	0.971	100	0.168
3.458-3.989	0.148	133	0.15	2241	0.15	2374	0.978	0.975	100	0.166
3.989-4.877	0.149	106	0.128	1912	0.129	2018	0.976	0.981	100	0.149
4.877-6.858	0.178	76	0.151	1522	0.152	1598	0.975	0.977	100	0.172
6.858-46.076	0.215	52	0.183	895	0.185	954	0.957	0.96	99.2663	0.206

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