PDB-8by3: FimH lectin domain in complex with oligomannose-6

ID or keywords:

Entry

Database: PDB / ID: 8by3

Title

FimH lectin domain in complex with oligomannose-6

Components

Type 1 fimbrin D-mannose specific adhesin

Keywords

CELL ADHESION / Type-1 fimbriae / Escherichia coli / FimH / Adhesin / Lectin / Oligomannose / High-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 K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.186 Å

Authors

Bouckaert, J. / Bourenkov, G.P.

Funding support

European Union, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Structural insights into a cooperative switch between one and two FimH bacterial adhesins binding pauci- and high-mannose type N-glycan receptors.
Authors: Krammer, E.M. / Bridot, C. / Serna, S. / Echeverria, B. / Semwal, S. / Roubinet, B. / van Noort, K. / Wilbers, R.H.P. / Bourenkov, G. / de Ruyck, J. / Landemarre, L. / Reichardt, N. / Bouckaert, J.

History

Deposition	Dec 11, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2023	Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8by3.cif.gz	141.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8by3.ent.gz	111.6 KB	Display	PDB format
PDBx/mmJSON format	8by3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8by3_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	8by3_full_validation.pdf.gz	3.3 MB	Display
Data in XML	8by3_validation.xml.gz	27.4 KB	Display
Data in CIF	8by3_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/8by3 ftp://data.pdbj.org/pub/pdb/validation_reports/by/8by3	HTTPS FTP

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Related structure data

Related structure data	7bhdC 8bxyC 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

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

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

1

A: Type 1 fimbrin D-mannose specific adhesin

C: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
Evidence: gel filtration, Sauer, M. M., Jakob, R. P., Luber, T., Canonica, F., Navarra, G., Ernst, B., Unverzagt, C., Maier, T., and Glockshuber, R. (2019) Binding of the Bacterial Adhesin FimH to ...Evidence: gel filtration, Sauer, M. M., Jakob, R. P., Luber, T., Canonica, F., Navarra, G., Ernst, B., Unverzagt, C., Maier, T., and Glockshuber, R. (2019) Binding of the Bacterial Adhesin FimH to Its Natural, Multivalent High-Mannose Type Glycan Targets. J Am Chem Soc 141, 936-944
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type 1 fimbrin D-mannose specific adhesin

D: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
35.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	153.110, 153.110, 230.410
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

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	Auth asym-ID	Auth seq-ID
1	1	1	A	1 - 158
2	1	1	A	1 - 158
3	2	2	A	1 - 158
4	2	2	A	1 - 158
5	3	3	A	1 - 158
6	3	3	A	1 - 158
7	4	4	A	1 - 158
8	4	4	A	1 - 158
9	5	5	A	1 - 158
10	5	5	A	1 - 158
11	6	6	A	1 - 158
12	6	6	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 K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P08191

#2: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...

Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-NI / NICKEL (II) ION

Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / 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 / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 165 / 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: 5.54 Å³/Da / Density meas: 0.3 Mg/m³ / Density % sol: 77.79 % Description: small lentil-like crystals grown on a large beam
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1 M Lithium sulphate 100 mM Tris-HCl, pH 8.5 10 mM Nickel chloride 3% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2021 / Details: MD3 diffractometer
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3.186→114.925 Å / Num. obs: 24701 / % possible obs: 88.45 % / Observed criterion σ(I): 1.2 / Redundancy: 11.07 % / B_iso Wilson estimate: 69.74 Å² / CC_1/2: 0.9522 / R_merge(I) obs: 0.613 / R_pim(I) all: 0.188 / R_rim(I) all: 0.643 / Net I/σ(I): 4.977
Reflection shell	Resolution: 3.186→3.341 Å / Redundancy: 13.067 % / R_merge(I) obs: 1.767 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1209 / CC_1/2: 0.584 / R split: 0.502 / R_rim(I) all: 1.838 / % possible all: 34.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.186→114.925 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.878 / SU B: 17.795 / SU ML: 0.295 / Cross valid method: FREE R-VALUE / ESU R: 0.977 / ESU R Free: 0.378
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2381	1532	6.202 %
R_work	0.2045	23169	-
all	0.207	-	-
obs	-	24701	87.916 %

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: 61.211 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.521 Å²	-0.261 Å²	-0 Å²
2-	-	-0.521 Å²	0 Å²
3-	-	-	1.691 Å²

Refinement step

Cycle: LAST / Resolution: 3.186→114.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4784	0	204	165	5153

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	5141
X-RAY DIFFRACTION	r_bond_other_d	0.032	0.017	4452
X-RAY DIFFRACTION	r_angle_refined_deg	1.561	1.683	7066
X-RAY DIFFRACTION	r_angle_other_deg	1.5	1.575	10404
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.543	5	628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.211	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.77	10	672
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	18.155	10	204
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	870
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5652
X-RAY DIFFRACTION	r_gen_planes_other	0.015	0.02	980
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	792
X-RAY DIFFRACTION	r_symmetry_nbd_other	1.042	0.2	13193
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	2480
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2245
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	168
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.022	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.223	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.314	0.2	127
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.303	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	5.302	6.718	2524
X-RAY DIFFRACTION	r_mcbond_other	5.299	6.718	2524
X-RAY DIFFRACTION	r_mcangle_it	7.365	10.064	3148
X-RAY DIFFRACTION	r_mcangle_other	7.365	10.066	3149
X-RAY DIFFRACTION	r_scbond_it	6.475	6.963	2617
X-RAY DIFFRACTION	r_scbond_other	6.473	6.963	2618
X-RAY DIFFRACTION	r_scangle_it	8.107	10.374	3918
X-RAY DIFFRACTION	r_scangle_other	8.106	10.374	3919
X-RAY DIFFRACTION	r_lrange_it	9.711	95.37	5226
X-RAY DIFFRACTION	r_lrange_other	9.711	95.37	5226
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.129	0.05	4555
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.118	0.05	4573
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.114	0.05	4570
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.128	0.05	4516
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.13	0.05	4484
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.096	0.05	4635

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	0.12914	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12914	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11802	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11802	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11409	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11409	0.05007
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12776	0.05007
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12776	0.05007
5	9	A	X-RAY DIFFRACTION	Local ncs	0.12952	0.05007
5	10	A	X-RAY DIFFRACTION	Local ncs	0.12952	0.05007
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09609	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09609	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 (%)
3.186-3.239	0.282	27	0.271	489	X-RAY DIFFRACTION	25.3189
3.239-3.328	0.293	58	0.268	850	X-RAY DIFFRACTION	45.7431
3.328-3.425	0.303	71	0.266	1244	X-RAY DIFFRACTION	68.5968
3.425-3.53	0.286	107	0.274	1606	X-RAY DIFFRACTION	92.0473
3.53-3.646	0.306	114	0.255	1712	X-RAY DIFFRACTION	99.4012
3.646-3.773	0.24	109	0.245	1634	X-RAY DIFFRACTION	100
3.773-3.916	0.228	107	0.23	1610	X-RAY DIFFRACTION	100
3.916-4.075	0.247	102	0.204	1534	X-RAY DIFFRACTION	100
4.075-4.256	0.246	100	0.189	1496	X-RAY DIFFRACTION	99.9374
4.256-4.464	0.213	94	0.184	1406	X-RAY DIFFRACTION	99.734
4.464-4.705	0.227	90	0.171	1360	X-RAY DIFFRACTION	100
4.705-4.99	0.189	86	0.163	1282	X-RAY DIFFRACTION	99.927
4.99-5.333	0.22	84	0.179	1224	X-RAY DIFFRACTION	100
5.333-5.76	0.243	78	0.188	1135	X-RAY DIFFRACTION	100
5.76-6.308	0.228	70	0.198	1059	X-RAY DIFFRACTION	100
6.308-7.05	0.227	65	0.194	964	X-RAY DIFFRACTION	99.9029
7.05-8.135	0.24	58	0.184	862	X-RAY DIFFRACTION	99.8914
8.135-9.951	0.165	46	0.164	731	X-RAY DIFFRACTION	98.6041
9.951-14.021	0.171	40	0.172	603	X-RAY DIFFRACTION	99.8447
14.021-114.925	0.407	26	0.311	368	X-RAY DIFFRACTION	98.2544

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