PDB-4xo8: Crystal structure of the FimH lectin domain from E.coli K12 in co...

ID or keywords:

Entry

Database: PDB / ID: 4xo8

Title

Crystal structure of the FimH lectin domain from E.coli K12 in complex with heptyl alpha-D-mannopyrannoside

Components

Protein FimH

Keywords

CELL ADHESION / type I pilus / lectin / UPEC / Bacterial Adhesin / mannose / UTI / catch bond

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: 1.698 Å

Authors

Jakob, R.P. / Eras, J. / Navarra, G. / Ernst, B. / Glockshuber, R. / Maier, T.

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	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.mon_nstd_flag / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xo8.cif.gz	194.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4xo8.ent.gz	158.5 KB	Display	PDB format
PDBx/mmJSON format	4xo8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4xo8_validation.pdf.gz	412 KB	Display	wwPDB validaton report
Full document	4xo8_full_validation.pdf.gz	412 KB	Display
Data in XML	4xo8_validation.xml.gz	18.1 KB	Display
Data in CIF	4xo8_validation.cif.gz	27.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xo/4xo8 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xo8	HTTPS FTP

-
Related structure data

Related structure data	4xo9C 4xoaC 4xobC 4xocC 4xodC 4xoeC 3mcyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x50-1 5fwr-3 6g2r-2 4av4-d 5fwr-8 7ayn-4 6gtx-1 5cgb-1 5fwr-7 1tr7-1 5l4x-2 3zl2-d 5l4w-2 6g2s-1 5muc-1 4x5p-d 5fwr-1 6gty-1 6g2s-8 4att-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

-
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)	62.970, 68.390, 95.940
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 / Fragment: lectin domain, UNP residues 22-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTrc / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#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: isolated from a genetically manipulated source Formula: C₁₃H₂₆O₆ / Comment: detergent*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.5 M (NH4)2SO4, 0.2 M Na Acetate pH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.698→52.644 Å / Num. obs: 45016 / % possible obs: 96.7 % / Redundancy: 11.5 % / R_merge(I) obs: 0.121 / Net I/σ(I): 14.3
Reflection shell	Resolution: 1.698→1.76 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.242 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5224 / % possible all: 79.3

-
Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1435)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3mcy

3mcy

Resolution: 1.698→52.644 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1954	2252	5 %	Random selection
R_work	0.1707	-	-	-
obs	0.1719	45016	96.85 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.698→52.644 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2392	0	38	471	2901

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2512
X-RAY DIFFRACTION	f_angle_d	1.018	3455
X-RAY DIFFRACTION	f_dihedral_angle_d	10.635	869
X-RAY DIFFRACTION	f_chiral_restr	0.037	409
X-RAY DIFFRACTION	f_plane_restr	0.004	443

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 (%)
1.698-1.7349	0.3767	110	0.3765	2087	X-RAY DIFFRACTION	77
1.7349-1.7753	0.3539	122	0.3269	2331	X-RAY DIFFRACTION	86
1.7753-1.8197	0.2922	135	0.2808	2560	X-RAY DIFFRACTION	93
1.8197-1.8689	0.2619	138	0.2291	2621	X-RAY DIFFRACTION	97
1.8689-1.9239	0.2078	143	0.1969	2710	X-RAY DIFFRACTION	99
1.9239-1.986	0.2071	142	0.1714	2703	X-RAY DIFFRACTION	99
1.986-2.0569	0.1826	144	0.1704	2724	X-RAY DIFFRACTION	100
2.0569-2.1393	0.1816	144	0.1496	2749	X-RAY DIFFRACTION	100
2.1393-2.2367	0.1656	143	0.1469	2705	X-RAY DIFFRACTION	100
2.2367-2.3546	0.1887	145	0.1495	2769	X-RAY DIFFRACTION	100
2.3546-2.5021	0.1882	144	0.1504	2733	X-RAY DIFFRACTION	100
2.5021-2.6953	0.1942	145	0.156	2749	X-RAY DIFFRACTION	100
2.6953-2.9665	0.1711	146	0.1535	2773	X-RAY DIFFRACTION	100
2.9665-3.3957	0.1846	146	0.1555	2776	X-RAY DIFFRACTION	100
3.3957-4.2779	0.1706	150	0.1466	2839	X-RAY DIFFRACTION	100
4.2779-52.644	0.1953	155	0.1786	2935	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	2.5306	0.272	-0.0097	2.8096	1.1622	4.3853	0.2047	-0.278	0.4335	0.2002	-0.082	-0.0688	-0.448	0.231	-0.1707	0.1982	-0.0329	0.0345	0.1968	-0.0267	0.2095	-14.2543	-0.0751	-2.7508
2	0.6016	0.1421	0.5252	1.1433	0.7857	2.4692	0.1532	-0.0317	0.067	0.0647	-0.0082	-0.0427	-0.3986	0.0206	-0.137	0.2032	-0.0227	0.0093	0.147	-0.0007	0.1808	-14.3162	-0.7917	18.082
3	0.0144	-0.1214	0.7019	0.437	-0.8515	4.0628	0.0396	-0.0113	0.0292	-0.0202	0.1505	0.0261	-0.3029	-0.0948	-0.204	0.2117	-0.0202	-0.0031	0.211	0.005	0.2165	-22.8464	-1.3028	0.2014
4	1.3372	0.2234	1.6411	0.8699	-0.1112	4.0889	0.0549	0.0809	-0.0659	0.0604	0.034	-0.0644	0.169	0.1251	-0.1073	0.168	-0.0093	0.0019	0.1407	-0	0.1671	-18.4299	-11.4988	11.3103
5	1.1377	-0.4962	0.6093	1.7041	-2.2961	3.0692	0.0643	-0.0317	-0.1123	-0.1665	0.1731	0.2255	0.2536	-0.2678	-0.1863	0.182	-0.0083	-0.0199	0.1776	0.0186	0.2016	-25.4365	-12.9052	6.8858
6	0.5585	-0.1825	1.4182	0.523	-0.9011	3.81	0.0251	-0.0345	0.0654	0.0116	-0.0403	-0.0358	0.0062	-0.025	0.0275	0.1581	0.0086	0.0171	0.1687	0.0112	0.1888	-22.1312	-4.2542	10.6379
7	2.4718	1.0925	-2.7123	0.8559	-1.2632	2.9881	-0.0286	-0.2022	0.0817	0.026	0.0905	-0.0916	0.0724	0.6355	-0.1102	0.1858	-0.0275	0.0021	0.2573	0.0021	0.2095	-6.9712	-3.48	22.9685
8	2.0495	0.5462	3.292	0.4899	0.5539	5.8724	0.2162	0.0245	-0.0118	0.0104	-0.0619	0.0019	0.5187	-0.0645	-0.1233	0.2076	0.0013	0.0032	0.1699	-0.0083	0.1686	-16.5571	-10.4007	2.5882
9	0.2553	0.0447	0.1814	0.6575	-0.1348	2.2118	0.067	0.0041	-0.0467	-0.0863	0.0641	-0.0966	-0.0766	0.2407	-0.1315	0.1766	0.0036	0.0256	0.1831	-0.0123	0.1829	-14.491	-6.6433	6.2012
10	2.6688	0.4401	-0.2733	3.1462	-1.6814	5.2266	0.1893	-0.2563	-0.6162	-0.0188	-0.0408	0.1273	0.4758	-0.3243	-0.1231	0.1654	-0.0363	-0.022	0.1743	0.0405	0.2341	-48.5966	0.0863	4.0176
11	0.8033	0.0313	-0.3288	0.9558	-1.0169	3.5497	0.1775	0.0356	-0.1568	0.0136	0.0359	0.0614	0.5655	-0.0005	-0.139	0.1605	-0.0134	0.0058	0.1417	-0.0075	0.1981	-48.8337	0.7854	24.872
12	-0.0423	0.0129	-0.7009	0.1342	0.7322	3.9976	0.0459	0.0102	-0.0035	0.023	0.0827	0.0329	0.3941	0.0641	-0.0804	0.1601	0.0071	0.0106	0.1789	-0.0066	0.1629	-40.0388	1.1633	7.1271
13	1.4069	0.4086	-1.5422	0.8315	0.2931	4.6247	0.14	0.0387	0.0715	0.0478	0.0468	0.0568	-0.2944	0.018	-0.1604	0.1481	-0.0055	0.0075	0.1071	-0.0047	0.155	-44.5723	11.4086	18.3657
14	1.2075	-1.0281	-0.8139	1.8167	2.2089	3.1475	0.0863	-0.0824	0.1326	-0.1195	0.2084	-0.2553	-0.293	0.3751	-0.3034	0.197	-0.0237	0.0234	0.2034	-0.0358	0.2045	-37.3208	12.6872	13.8454
15	0.6378	-0.3161	-1.0682	0.5544	0.9146	4.2677	-0.0095	-0.0949	-0.0542	0.0183	0.0267	0.0156	0.174	0.3881	-0.03	0.1737	0.01	0.0086	0.1891	-0.0102	0.1968	-40.9501	3.94	17.5619
16	2.9624	1.318	3.0179	1.1777	1.4149	3.0819	0.0512	-0.2961	-0.0701	-0.0041	0.0083	0.3179	-0.0977	-0.8287	0.039	0.1454	-0.0134	0.0071	0.1928	0.0039	0.2032	-56.1996	3.6022	29.6959
17	2.3069	0.1255	-3.316	0.4054	-0.4679	5.7363	0.2647	0.0513	0.1016	0.0399	-0.0303	0.0191	-0.5205	-0.0402	-0.1177	0.1695	-0.0184	0.0155	0.1426	-0.003	0.1583	-46.1405	10.3525	9.4512
18	0.2705	-0.1329	-0.0553	0.4368	-0.1455	1.6073	0.0895	-0.012	0.0214	-0.0193	0.0006	0.0481	-0.0676	-0.1227	-0.0974	0.1544	-0.0152	-0.005	0.1646	-0.0049	0.1614	-48.3089	6.6432	13.032

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 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 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 116 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 117 through 124 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 125 through 135 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 136 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 15 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 16 through 32 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 33 through 53 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 54 through 77 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 78 through 95 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 96 through 116 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 117 through 124 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 125 through 135 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 136 through 158 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi