PDB-8bvd: FimH lectin domain in complex with mannose C-linked to quinoline

ID or keywords:

Entry

Database: PDB / ID: 8bvd

Title

FimH lectin domain in complex with mannose C-linked to quinoline

Components

Type 1 fimbrin D-mannose specific adhesin

Keywords

CELL ADHESION / Type-1 fimbriae / Escherichia coli / FimH / Adhesin / Lectin / Anti-adhesives / C-linked mannose

Function / homology

Function and homology information

pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function

Biological species

Escherichia coli UTI89 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.995 Å

Authors

Bouckaert, J. / Bridot, C.

Funding support

France,

Canada, 2items

Citation

Journal: Pharmaceutics / Year: 2023
Title: Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists.
Authors: Mousavifar, L. / Sarshar, M. / Bridot, C. / Scribano, D. / Ambrosi, C. / Palamara, A.T. / Vergoten, G. / Roubinet, B. / Landemarre, L. / Bouckaert, J. / Roy, R.

History

Deposition	Dec 3, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2023	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8bvd.cif.gz	140.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8bvd.ent.gz	110.2 KB	Display	PDB format
PDBx/mmJSON format	8bvd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8bvd_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8bvd_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8bvd_validation.xml.gz	30.9 KB	Display
Data in CIF	8bvd_validation.cif.gz	40.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bv/8bvd ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bvd	HTTPS FTP

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Related structure data

Related structure data	5abz
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

A: Type 1 fimbrin D-mannose specific adhesin

B: Type 1 fimbrin D-mannose specific adhesin

C: Type 1 fimbrin D-mannose specific adhesin

D: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

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

1

A: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
Evidence: surface plasmon resonance, The assembly is one chain with one ligand.
17.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
17.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
17.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
17.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	151.784, 151.784, 225.034
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	B-322- HOH
2	1	B-382- HOH
3	1	C-328- HOH
4	1	D-316- HOH

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:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 158
2	1	1	1	A	1 - 158
3	2	2	1	A	1 - 158
4	2	2	1	A	1 - 158
5	3	3	1	A	1 - 158
6	3	3	1	A	1 - 158
7	4	4	1	A	1 - 158
8	4	4	1	A	1 - 158
9	5	5	1	A	1 - 158
10	5	5	1	A	1 - 158
11	6	6	1	A	1 - 158
12	6	6	1	A	1 - 158

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	Type 1 fimbrin D-mannose specific adhesin / Protein FimH Mass: 16916.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89 / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P08191
#2: Chemical	ChemComp-RLO / (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-[(E)-3-quinolin-6-ylprop-2-enyl]oxane-3,4,5-triol / (2R,3S,4R,5S,6R)-2-(hydroxymethyl)-6-((E)-3-(quinolin-6-yl)allyl)tetrahydro-2H-pyran-3,4,5-triol Mass: 331.363 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₈H₂₁NO₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / 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: 5.53 Å³/Da / Density % sol: 77.75 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 3.0M NaCl and 0.1M BIS-TRIS at pH=5.5 / PH range: 5.25 - 5.75

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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: Sep 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 2.995→49.732 Å / Num. obs: 31057 / % possible obs: 98.6 % / Redundancy: 39.4 % / CC_1/2: 0.996 / R_rim(I) all: 0.464 / Net I/σ(I): 12.41
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 40.2 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4900 / CC_1/2: 0.615 / R_rim(I) all: 3.422 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.995→49.732 Å / Cor.coef. F_o:F_c: 0.881 / Cor.coef. F_o:F_c free: 0.83 / WR_factor R_free: 0.243 / WR_factor R_work: 0.206 / SU B: 17.437 / SU ML: 0.302 / Average fsc free: 0.9258 / Average fsc work: 0.9484 / Cross valid method: THROUGHOUT / ESU R: 0.669 / ESU R Free: 0.41
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3034	1439	4.974 %	RANDOM
R_work	0.2512	27492	-	-
all	0.254	-	-	-
obs	-	28931	91.874 %	-

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: 53.611 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.117 Å²	-0.059 Å²	-0 Å²
2-	-	-0.117 Å²	0 Å²
3-	-	-	0.381 Å²

Refinement step

Cycle: LAST / Resolution: 2.995→49.732 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4784	0	96	224	5104

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.011	5008
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.016	4388
X-RAY DIFFRACTION	r_angle_refined_deg	1.387	1.669	6888
X-RAY DIFFRACTION	r_angle_other_deg	0.506	1.568	10208
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.665	5	628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.735	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.291	10	672
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.377	10	204
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	808
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5680
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	996
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	929
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	4288
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2359
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	2730
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.227	0.2	204
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.091	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.118	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.251	0.2	128
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.2	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	5.497	5.873	2524
X-RAY DIFFRACTION	r_mcbond_other	5.494	5.873	2524
X-RAY DIFFRACTION	r_mcangle_it	8.352	8.766	3148
X-RAY DIFFRACTION	r_mcangle_other	8.35	8.768	3149
X-RAY DIFFRACTION	r_scbond_it	4.698	5.816	2484
X-RAY DIFFRACTION	r_scbond_other	4.697	5.815	2485
X-RAY DIFFRACTION	r_scangle_it	7.264	8.65	3740
X-RAY DIFFRACTION	r_scangle_other	7.264	8.65	3741
X-RAY DIFFRACTION	r_lrange_it	11.972	69.583	5355
X-RAY DIFFRACTION	r_lrange_other	11.971	69.577	5356
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.145	0.05	4519
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.138	0.05	4639
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.119	0.05	4804
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.14	0.05	4638
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.15	0.05	4555
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.122	0.05	4739

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	0.14491	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.14491	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13789	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13789	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11854	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11854	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.13999	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.13999	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.15045	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.15045	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12229	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12229	0.05009

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
2.995-3.073	0.35	34	0.315	756	0.316	2255	0.915	0.93	35.0333	0.291
3.073-3.157	0.415	75	0.34	1465	0.344	2237	0.894	0.914	68.8422	0.317
3.157-3.248	0.469	101	0.325	1912	0.331	2139	0.85	0.923	94.1094	0.295
3.248-3.348	0.389	105	0.284	1992	0.29	2099	0.896	0.939	99.9047	0.248
3.348-3.457	0.415	100	0.341	1895	0.345	2045	0.876	0.915	97.555	0.296
3.457-3.577	0.362	97	0.29	1854	0.293	1960	0.919	0.942	99.5408	0.256
3.577-3.712	0.352	92	0.34	1737	0.341	1916	0.925	0.919	95.4593	0.298
3.712-3.862	0.317	92	0.267	1748	0.269	1840	0.926	0.952	100	0.233
3.862-4.033	0.349	82	0.304	1583	0.306	1767	0.919	0.938	94.2275	0.256
4.033-4.229	0.25	85	0.202	1617	0.205	1702	0.956	0.974	100	0.174
4.229-4.456	0.266	81	0.191	1544	0.195	1625	0.957	0.976	100	0.165
4.456-4.723	0.235	77	0.19	1456	0.193	1533	0.967	0.977	100	0.165
4.723-5.046	0.211	73	0.186	1383	0.187	1456	0.973	0.978	100	0.16
5.046-5.446	0.206	68	0.196	1292	0.197	1360	0.974	0.974	100	0.171
5.446-5.959	0.273	63	0.219	1192	0.221	1255	0.946	0.966	100	0.192
5.959-6.65	0.313	58	0.236	1104	0.24	1162	0.928	0.961	100	0.205
6.65-7.656	0.264	51	0.23	979	0.232	1030	0.96	0.964	100	0.202
7.656-9.322	0.277	45	0.23	852	0.232	897	0.95	0.965	100	0.212
9.322-12.957	0.281	36	0.224	687	0.227	723	0.942	0.962	100	0.208
12.957-49.732	0.294	24	0.298	444	0.298	468	0.923	0.94	100	0.279

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