PDB-4xoc: Crystal structure of the FimH lectin domain from E.coli F18 in co...

ID or keywords:

Entry

Database: PDB / ID: 4xoc

Title

Crystal structure of the FimH lectin domain from E.coli F18 in complex with heptyl alpha-D-mannopyrannoside

Components

FimH protein

Keywords

CELL ADHESION / type I pilus / catch-bond /

lectin / UPEC /

bacterial adhesin / UTI /

mannose /

isomerase

Function / homology

Function and homology information

pilus /

cell adhesion
Similarity search - Function

Biological species

Escherichia coli O6:K15:H31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

Jakob, R.P. / Sauer, M.M. / Navarra, G. / Ernst, B. / Glockshuber, R. / Maier, T.

Funding support

Switzerland, 2items

Citation

Journal: Nat Commun / Year: 2016
Title: Catch-bond mechanism of the bacterial adhesin FimH.
Authors: Sauer, M.M. / Jakob, R.P. / Eras, J. / Baday, S. / Eris, D. / Navarra, G. / Berneche, S. / Ernst, B. / Maier, T. / Glockshuber, R.

History

Deposition	Jan 16, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 2.0	Sep 13, 2017	Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.label_alt_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 3.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xoc.cif.gz	198.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4xoc.ent.gz	163.8 KB	Display	PDB format
PDBx/mmJSON format	4xoc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xo/4xoc ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xoc	HTTPS FTP

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Related structure data

Related structure data	4xo8C 4xo9C 4xoaC 4xobC 4xodC 4xoeC 3mcyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5l4t-2 5l4t-1 5l4u-1 4avi-1 7ayn-3 6gtw-1 5abz-2 5l4v-2 4lov-d 5jcr-1 5l4v-3 5l4w-3 5l4x-1 6gtw-2 4avj-2 4buq-2 6g2s-2 4av0-2 4avj-1 4x50-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: FimH protein

B: FimH protein

hetero molecules

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

1

A: FimH protein

hetero molecules

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

2

B: FimH protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	140.070, 176.056, 28.330
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-501- KGM
2	1	B-501- KGM
3	1	A-613- HOH
4	1	A-807- HOH
5	1	A-880- HOH
6	1	B-842- HOH

#1: Protein	FimH protein Mass: 16945.826 Da / Num. of mol.: 2 / Fragment: UNP residues 25-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:K15:H31 (bacteria) / Strain: F18 / Gene: ECP_4655 / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: Q0T8Y8, UniProt: A0A454AB91*PLUS
#2: Sugar	ChemComp-KGM / heptyl alpha-D-mannopyranoside / Heptyl Alpha-D-mannopyrannoside / heptyl alpha-D-mannoside / heptyl D-mannoside / heptyl mannoside Type: D-saccharide / Mass: 278.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₆O₆ / Comment: detergent*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 17 % PEG2000MME, 0.1M Hepes pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.36246 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.36246 Å / Relative weight: 1
Reflection	Resolution: 1.42→54.806 Å / Num. obs: 66393 / % possible obs: 98.9 % / Redundancy: 16.9 % / R_merge(I) obs: 0.117 / Net I/σ(I): 18
Reflection shell	Resolution: 1.42→1.51 Å / Redundancy: 13.4 % / R_merge(I) obs: 1.118 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 11128 / Num. unique all: 11128 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XSCALE		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3mcy

3mcy

Resolution: 1.42→54.806 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1745	3319	5 %	Random
R_work	0.1483	-	-	-
obs	0.1496	66393	98.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.42→54.806 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2391	0	38	596	3025

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	2554
X-RAY DIFFRACTION	f_angle_d	1.615	3513
X-RAY DIFFRACTION	f_dihedral_angle_d	11.214	882
X-RAY DIFFRACTION	f_chiral_restr	0.077	415
X-RAY DIFFRACTION	f_plane_restr	0.009	450

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 (%)
1.4201-1.4404	0.2711	128	0.2591	2432	X-RAY DIFFRACTION	94
1.4404-1.4619	0.2494	131	0.2308	2488	X-RAY DIFFRACTION	95
1.4619-1.4847	0.2278	132	0.2207	2514	X-RAY DIFFRACTION	95
1.4847-1.509	0.2141	135	0.2111	2567	X-RAY DIFFRACTION	99
1.509-1.5351	0.2167	136	0.1955	2587	X-RAY DIFFRACTION	100
1.5351-1.563	0.2244	139	0.1787	2627	X-RAY DIFFRACTION	99
1.563-1.593	0.2364	134	0.1737	2550	X-RAY DIFFRACTION	98
1.593-1.6256	0.2017	137	0.1736	2599	X-RAY DIFFRACTION	100
1.6256-1.6609	0.1871	139	0.167	2648	X-RAY DIFFRACTION	99
1.6609-1.6996	0.1993	135	0.1609	2572	X-RAY DIFFRACTION	99
1.6996-1.7421	0.1693	138	0.1569	2627	X-RAY DIFFRACTION	100
1.7421-1.7892	0.1837	138	0.1454	2603	X-RAY DIFFRACTION	98
1.7892-1.8418	0.1661	137	0.1459	2619	X-RAY DIFFRACTION	100
1.8418-1.9013	0.1778	140	0.1394	2662	X-RAY DIFFRACTION	99
1.9013-1.9692	0.148	137	0.1301	2603	X-RAY DIFFRACTION	100
1.9692-2.0481	0.1411	141	0.128	2668	X-RAY DIFFRACTION	100
2.0481-2.1413	0.1628	138	0.1301	2630	X-RAY DIFFRACTION	100
2.1413-2.2542	0.1428	140	0.1238	2663	X-RAY DIFFRACTION	100
2.2542-2.3954	0.1738	142	0.1316	2682	X-RAY DIFFRACTION	100
2.3954-2.5804	0.1622	142	0.1365	2702	X-RAY DIFFRACTION	100
2.5804-2.84	0.1764	140	0.1438	2672	X-RAY DIFFRACTION	100
2.84-3.2509	0.1817	142	0.1384	2697	X-RAY DIFFRACTION	100
3.2509-4.0956	0.1558	146	0.1389	2767	X-RAY DIFFRACTION	100
4.0956-54.8464	0.1706	152	0.1549	2895	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.2627	-1.5264	1.2433	4.939	-0.3543	3.9311	0.1149	0.206	0.034	-0.4521	-0.1659	-0.3803	0.1388	0.2561	0.0262	0.1395	0.0114	0.038	0.091	0.0171	0.0951	-49.9243	-14.146	-0.8029
2	0.3727	-0.3519	-0.0777	0.791	0.1089	0.3849	0.0004	0.0139	0.0284	-0.0631	-0.0122	0.0214	0.046	0.0159	0.009	0.0842	0.0059	-0.0067	0.0985	-0.0013	0.0735	-48.9664	-32.5358	5.1807
3	1.7978	-2.3563	-0.5788	4.9136	0.5941	0.9711	-0.0451	-0.0336	0.0595	0.1114	0.0299	-0.1123	-0.0516	0.0712	-0.0025	0.0942	-0.0023	-0.0059	0.0812	-0.0008	0.0865	-52.0099	-7.6099	7.2562
4	0.1687	-0.5337	-0.2025	4.0812	1.5239	0.9684	-0.0114	0.0233	-0.0762	-0.1452	-0.0253	0.2488	-0.0312	-0.0635	0.0481	0.0645	-0.0054	-0.0101	0.0955	0.0065	0.1144	-59.7477	-28.6723	5.9461
5	1.5228	1.0572	0.266	2.2484	-0.3607	0.8785	0.0278	-0.0683	-0.0152	0.1879	0.0297	0.1861	0.0092	-0.0626	-0.0491	0.0941	0.0032	0.0101	0.0882	0.0094	0.1097	-61.5809	-22.8618	12.3134
6	0.8803	0.4317	0.2049	5.585	0.1577	0.5187	-0.0157	-0.03	0.0289	0.1134	-0.0488	-0.2823	-0.0776	-0.0047	0.0686	0.0803	0.0032	-0.0032	0.0931	0.0029	0.0852	-51.7527	-21.249	10.2887
7	3.6183	-1.1242	-1.5831	1.4515	0.8137	2.6563	-0.2255	0.1371	-0.2935	-0.1823	0.1574	0.2939	0.5508	-0.2827	0.1024	0.1304	-0.0266	-0.0098	0.1123	-0.0177	0.1055	-52.8538	-43.9188	0.6111
8	0.6934	-1.2567	-0.1897	2.9406	0.481	0.2972	0.0251	0.0293	-0.0516	-0.08	-0.0367	0.1974	-0.022	-0.0242	0.0039	0.0922	0.0009	-0.0122	0.0768	0.0065	0.063	-56.804	-22.44	1.7465
9	5.2833	0.8059	-2.6171	3.0044	0.4485	4.3237	-0.1744	-0.3331	-0.4048	0.1734	-0.0069	-0.354	0.3637	0.2802	0.1995	0.1383	0.0117	-0.0056	0.1383	0.0191	0.2037	-10.6865	-22.8734	12.4597
10	2.3291	1.2342	-0.3089	0.806	-0.2522	0.289	0.1045	-0.2599	0.0966	0.0273	-0.1091	-0.0852	-0.0193	0.089	-0.0028	0.1124	0.0025	-0.0053	0.1275	0.0002	0.1144	-28.8743	-28.1186	16.4659
11	2.5112	1.2278	-0.713	3.2102	-0.9209	1.8469	-0.0075	-0.1018	0.2116	-0.0072	0.0419	-0.1181	0.0306	0.0937	-0.0414	0.1003	-0.0102	-0.0076	0.1183	-0.0158	0.1742	-9.2548	-12.5281	13.6491
12	3.5666	4.3772	0.2532	5.4894	0.2811	0.6803	-0.3211	0.2303	0.2054	-0.5647	0.2898	0.0104	-0.1247	0.0466	0.0058	0.1232	-0.0102	-0.0008	0.1307	0.0139	0.151	-22.1383	-18.014	4.5018
13	2.0861	1.5722	0.0744	1.3948	-0.0126	0.134	0.0615	-0.0485	0.3639	0.0588	-0.0629	0.1743	-0.0443	0.024	0.0003	0.1186	-0.0056	-0.0018	0.131	-0.0184	0.1776	-27.2366	-17.8618	10.5834
14	4.6566	0.2609	1.011	0.023	0.0483	0.2274	0.0397	0.0493	-0.1542	-0.0182	-0.0492	-0.0902	0.0444	0.0612	0.0078	0.0807	0.0133	-0.0061	0.0934	0.0035	0.0716	-37.0124	-37.2311	11.7958
15	1.4396	1.0504	-0.1254	1.0807	-0.0178	0.3071	-0.1421	0.153	0.0521	-0.1298	0.1423	-0.1068	-0.0113	-0.0042	0.0053	0.0837	0.001	-0.0046	0.1059	0.0081	0.1082	-20.473	-22.8766	7.5443

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 40 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 77 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 78 through 95 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 96 through 111 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 112 through 124 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 125 through 158 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 15 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 16 through 40 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 41 through 53 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 54 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 111 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 112 through 124 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 125 through 158 )

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