PDB-5l4x: Crystal structure of FimH lectin domain in complex with 4-Deoxy-H...

ID or keywords:

Entry

Database: PDB / ID: 5l4x

Title

Crystal structure of FimH lectin domain in complex with 4-Deoxy-Heptylmannoside

Components

Protein FimH

Keywords

SUGAR BINDING PROTEIN / FimH / Type 1 pilus / urinary tract infection / UTI / carbohydrate / lectin / mannose / cell adhesion

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 (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Jakob, R.P. / Zihlmann, P. / Rabbani, S. / Maier, T. / Ernst, B.

Citation

Journal: To Be Published
Title: High-Affinity Carbohydrate-Lectin Interactions: How Nature Makes it Possible
Authors: Zihlmann, P. / Jiang, X. / Sager, C.P. / Fiege, B. / Jakob, R.P. / Siegrist, S. / Zalewski, A. / Rabbani, S. / Eris, D. / Silbermann, M. / Pang, L. / Muhlethaler, T. / Sharpe, T. / Maier, T. / Ernst, B.

History

Deposition	May 26, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2017	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / 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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	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
Revision 2.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5l4x.cif.gz	191.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5l4x.ent.gz	155.9 KB	Display	PDB format
PDBx/mmJSON format	5l4x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5l4x_validation.pdf.gz	649.3 KB	Display	wwPDB validaton report
Full document	5l4x_full_validation.pdf.gz	649.4 KB	Display
Data in XML	5l4x_validation.xml.gz	17.8 KB	Display
Data in CIF	5l4x_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l4/5l4x ftp://data.pdbj.org/pub/pdb/validation_reports/l4/5l4x	HTTPS FTP

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Related structure data

Related structure data	5l4tC 5l4uC 5l4vC 5l4wC 5l4yC 4xo8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5l4v-2 4avj-1 5l4y-1 4lov-d 5l4w-3 5fwr-4 5l4t-1 4buq-1 6gty-3 5l4t-2 6gtw-2 5l4v-1 4avi-1 4av0-2 5f3f-d 7ayn-3 5abz-2 5fwr-1 4avj-2 1uwf-d 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

Deposited unit

A: Protein FimH

B: Protein FimH

hetero molecules

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

1

A: Protein FimH

hetero molecules

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

2

B: Protein FimH

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)	61.079, 68.380, 95.629
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protein FimH Mass: 16916.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Sugar	ChemComp-6KU / heptyl 4-deoxy-4-deoxy-alpha-D-mannopyranoside / 4-Deoxy-Heptylmannoside / heptyl 4-deoxy-4-deoxy-alpha-D-mannoside / heptyl 4-deoxy-4-deoxy-D-mannoside / heptyl 4-deoxy-4-deoxy-mannoside Type: D-saccharide / Mass: 262.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₆O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.95 Å³/Da / Density % sol: 58.32 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7 and 25-30% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.9→32.194 Å / Num. obs: 60681 / % possible obs: 99.5 % / Redundancy: 6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.062 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.9→1.98 Å / Redundancy: 6 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	dev_1938	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XO8

4xo8

Resolution: 1.9→32.194 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.29

	R_factor	Num. reflection	% reflection
R_free	0.2045	2976	4.9 %
R_work	0.1768	-	-
obs	0.1781	60681	99.51 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.9→32.194 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2392	0	36	391	2819

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2490
X-RAY DIFFRACTION	f_angle_d	1.092	3420
X-RAY DIFFRACTION	f_dihedral_angle_d	11.517	872
X-RAY DIFFRACTION	f_chiral_restr	0.05	402
X-RAY DIFFRACTION	f_plane_restr	0.005	438

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 (%)
1.9001-1.9312	0.2819	142	0.2656	2732	X-RAY DIFFRACTION	99
1.9312-1.9645	0.2575	123	0.2421	2780	X-RAY DIFFRACTION	99
1.9645-2.0002	0.2551	145	0.2283	2717	X-RAY DIFFRACTION	99
2.0002-2.0387	0.1943	141	0.2273	2787	X-RAY DIFFRACTION	99
2.0387-2.0803	0.2202	131	0.2015	2713	X-RAY DIFFRACTION	99
2.0803-2.1255	0.2706	141	0.1925	2721	X-RAY DIFFRACTION	99
2.1255-2.175	0.2302	153	0.1843	2785	X-RAY DIFFRACTION	100
2.175-2.2293	0.1874	128	0.1757	2740	X-RAY DIFFRACTION	100
2.2293-2.2896	0.2155	140	0.174	2735	X-RAY DIFFRACTION	99
2.2896-2.357	0.2082	162	0.1665	2766	X-RAY DIFFRACTION	100
2.357-2.433	0.2362	133	0.1614	2731	X-RAY DIFFRACTION	100
2.433-2.5199	0.1665	146	0.1617	2761	X-RAY DIFFRACTION	100
2.5199-2.6208	0.2003	150	0.1655	2760	X-RAY DIFFRACTION	100
2.6208-2.74	0.1822	146	0.1648	2730	X-RAY DIFFRACTION	100
2.74-2.8844	0.2023	124	0.1746	2782	X-RAY DIFFRACTION	100
2.8844-3.065	0.2333	160	0.1683	2728	X-RAY DIFFRACTION	100
3.065-3.3014	0.2326	143	0.1768	2742	X-RAY DIFFRACTION	99
3.3014-3.6332	0.1728	142	0.1647	2760	X-RAY DIFFRACTION	100
3.6332-4.158	0.2054	133	0.1535	2768	X-RAY DIFFRACTION	100
4.158-5.235	0.159	128	0.1468	2743	X-RAY DIFFRACTION	99
5.235-32.1987	0.185	165	0.1977	2724	X-RAY DIFFRACTION	99

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	0.57	0.2687	0.9803	0.4638	0.309	1.6364	0.0406	0.0135	0.0787	0.0229	0.0128	0.0034	-0.4206	0.0445	-0.0623	0.2159	-0.0442	0.0049	0.1403	0.005	0.1925	-15.3913	-0.6451	10.595
2	0.403	0.1772	0.6112	0.7346	-1.1571	3.5997	-0.0114	0.0456	-0.0388	0.0403	0.0951	-0.0112	0.0716	-0.0879	-0.0844	0.1728	-0.0142	-0.0084	0.1513	-0.0091	0.1495	-20.0274	-7.691	4.6218
3	1.045	-0.7358	0.9376	1.5448	-1.4327	2.6697	0.1692	0.0277	-0.0703	-0.0667	0.1251	0.1725	0.4096	-0.3315	-0.2452	0.1965	-0.0301	-0.0151	0.1676	0.0309	0.1816	-24.9935	-13.0522	7.4828
4	0.4583	0.1545	0.461	0.5156	-0.0222	3.2841	0.0258	0.01	-0.0086	-0.0166	0.0344	-0.0147	0.0453	0.1281	-0.0808	0.1463	-0.0203	0.0085	0.1461	0.0099	0.1507	-16.1358	-6.1791	9.3922
5	2.558	0.1552	-0.265	2.5334	-1.9263	4.7957	-0.0536	-0.0825	-0.2828	-0.1019	-0.0269	0.0874	0.5139	-0.2587	0.0181	0.1764	-0.0268	-0.0119	0.1912	-0.0192	0.1838	-47.2658	0.3105	3.0924
6	0.444	-0.0421	-0.7754	0.6759	-0.6834	2.0878	0.1085	-0.0004	-0.0639	0.0431	-0.0101	0.0059	0.3168	0.063	0.0153	0.1878	-0.0456	0.0027	0.1808	-0.0168	0.2116	-47.2438	0.9391	23.9072
7	0.1398	-0.0242	-0.5943	0.2664	0.4194	3.0011	0.0077	0.0245	-0.081	0.0611	0.0253	-0.0987	0.2032	-0.1137	-0.0562	0.1589	-0.0056	-0.0093	0.1808	0.0047	0.1788	-38.7492	1.3581	6.0045
8	3.0375	-0.4482	-4.2584	1.0744	0.7638	6.7812	0.3109	0.3396	0.303	-0.042	0.0985	-0.1272	-0.5092	-0.3677	-0.2771	0.1716	-0.0028	0.0072	0.2149	-0.0012	0.1739	-42.4327	12.5179	9.8809
9	1.3913	1.0419	-1.1219	0.8106	-0.6676	4.2393	0.2011	-0.2363	0.072	0.0828	-0.0366	-0.1314	-0.0214	0.0744	-0.0469	0.1885	-0.019	-0.0029	0.1263	-0.0095	0.1612	-43.5621	10.4831	24.2643
10	0.8674	-0.8603	-0.9817	1.5497	1.8526	2.3828	0.1091	-0.0554	0.0118	-0.3217	0.1401	-0.1741	-0.3563	0.393	-0.1636	0.2223	-0.0417	0.0285	0.2161	-0.0277	0.223	-35.9856	12.8979	12.8514
11	0.5331	-0.7229	-1.6969	0.9699	2.2783	5.4526	-0.0493	0.0041	-0.146	-0.0709	-0.1434	-0.0039	0.4798	0.2114	-0.0826	0.1703	0.0168	0.0058	0.1701	0.0046	0.2273	-36.3289	-0.134	3.5544
12	0.9772	0.4052	-0.1377	1.1578	0.2951	2.1085	0.2056	-0.2299	0.1308	0.2123	-0.0967	0.0541	0.1094	0.0991	-0.0388	0.1878	-0.0135	0.001	0.1715	0.0149	0.1872	-47.1004	6.5975	28.8521
13	2.1813	0.5283	-3.5694	0.7512	-0.4734	6.9756	0.2659	-0.0698	-0.0114	0.0024	-0.1674	-0.1179	-0.7136	0.2617	-0.1757	0.1523	-0.0285	0.0123	0.1629	-0.007	0.1648	-44.8309	10.5266	8.5226
14	0.1424	0.1868	-0.1963	0.8088	-0.1701	1.7193	0.0493	0.0305	0.0193	-0.0713	0.0315	0.0019	0.0445	-0.1256	-0.0721	0.1246	0.023	-0.0105	0.1673	0.0006	0.1686	-47.0532	6.5832	12.3907

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 77 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 95 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 158 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 15 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 16 through 32 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 33 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 64 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 77 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 78 through 95 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 96 through 104 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 105 through 124 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 125 through 135 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 136 through 158 )

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