PDB-4xoa: Crystal structure of a FimH*DsG complex from E.coli K12 in space ...

ID or keywords:

Entry

Database: PDB / ID: 4xoa

Title

Crystal structure of a FimH*DsG complex from E.coli K12 in space group P1

Components

FimG
Protein FimH

Keywords

CELL ADHESION / type I pilus / catch-bond / lectin / UPEC / bacterial adhesin / UTI / mannose / isomerase

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: 2.541 Å

Authors

Jakob, R.P. / Eras, J. / 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 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xoa.cif.gz	603 KB	Display	PDBx/mmCIF format
PDB format	pdb4xoa.ent.gz	511.7 KB	Display	PDB format
PDBx/mmJSON format	4xoa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4xoa_validation.pdf.gz	447.9 KB	Display	wwPDB validaton report
Full document	4xoa_full_validation.pdf.gz	449.7 KB	Display
Data in XML	4xoa_validation.xml.gz	39.5 KB	Display
Data in CIF	4xoa_validation.cif.gz	55.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xo/4xoa ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xoa	HTTPS FTP

-
Related structure data

Related structure data	4xo8C 4xo9C 4xobC 4xocC 4xodC 4xoeC 1qunS 3mcyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jqi-1 4xo9-d 5jqi-2 4g8l-3 4g8l-4 5bq8-2 1786 5jqi-3 2y5q-d 3huf-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) 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

B: FimG

H: FimG

A: Protein FimH

D: FimG

C: Protein FimH

F: FimG

E: Protein FimH

G: Protein FimH

122 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: FimG

A: Protein FimH

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

2

H: FimG

G: Protein FimH

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

3

D: FimG

C: Protein FimH

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

4

F: FimG

E: Protein FimH

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

Unit cell

Length a, b, c (Å)	56.530, 77.624, 78.107
Angle α, β, γ (deg.)	101.54, 111.13, 96.29
Int Tables number	1
Space group name H-M	P1

#1: Protein/peptide	FimG Mass: 1416.661 Da / Num. of mol.: 4 / Fragment: UNP residues 24-37 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimG / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: C4ZT07, UniProt: P08190*PLUS
#2: Protein	Protein FimH Mass: 29081.314 Da / Num. of mol.: 4 / Fragment: UNP residues 22-300 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
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2M Na Malonate, 20%PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.541→52.674 Å / Num. obs: 35539 / % possible obs: 90.6 % / Redundancy: 3.4 % / R_merge(I) obs: 0.135 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.541→2.69 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / Num. unique all: 5844

-
Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1779)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3mcy, 1qun

3mcy

1qun

Resolution: 2.541→52.674 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2598	1999	5.62 %	Random selection
R_work	0.2398	-	-	-
obs	0.2409	35539	90.65 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.541→52.674 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8558	0	0	190	8748

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8742
X-RAY DIFFRACTION	f_angle_d	0.955	12002
X-RAY DIFFRACTION	f_dihedral_angle_d	12.552	2974
X-RAY DIFFRACTION	f_chiral_restr	0.036	1454
X-RAY DIFFRACTION	f_plane_restr	0.004	1558

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 (%)
2.5409-2.6044	0.3634	139	0.3226	2342	X-RAY DIFFRACTION	87
2.6044-2.6748	0.3634	149	0.3479	2500	X-RAY DIFFRACTION	95
2.6748-2.7535	0.3467	149	0.3145	2489	X-RAY DIFFRACTION	95
2.7535-2.8424	0.3186	151	0.2965	2532	X-RAY DIFFRACTION	95
2.8424-2.944	0.2904	150	0.2745	2518	X-RAY DIFFRACTION	96
2.944-3.0618	0.3083	150	0.2802	2517	X-RAY DIFFRACTION	96
3.0618-3.2012	0.2791	150	0.2679	2537	X-RAY DIFFRACTION	96
3.2012-3.3699	0.2968	152	0.2564	2544	X-RAY DIFFRACTION	95
3.3699-3.581	0.2872	143	0.2673	2406	X-RAY DIFFRACTION	92
3.581-3.8574	0.2982	87	0.2781	1448	X-RAY DIFFRACTION	55
3.8574-4.2455	0.2296	119	0.2061	2015	X-RAY DIFFRACTION	77
4.2455-4.8594	0.1943	155	0.17	2579	X-RAY DIFFRACTION	97
4.8594-6.1209	0.1956	151	0.1657	2542	X-RAY DIFFRACTION	97
6.1209-52.6853	0.1996	154	0.1839	2571	X-RAY DIFFRACTION	97

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	5.3303	0.964	-1.3845	5.9214	-3.9315	5.1537	-0.0297	0.0603	0.0001	-0.1799	-0.1081	-0.2949	0.0312	0.1898	0.1759	0.1339	-0.0849	0.1187	0.6884	0.0682	0.39	-6.1329	22.1846	39.3223
2	3.955	-0.5676	0.6678	8.022	-4.6492	4.1983	-0.102	0.0098	0.1094	0.0367	0.058	0.0593	-0.1492	-0.0647	-0.0093	0.0951	0.0696	-0.1345	0.5676	0.1738	0.3108	-20.0192	15.6736	-22.8665
3	1.7405	0.5193	-1.858	1.1888	-0.3594	3.0195	-0.2182	0.2597	-0.3184	-0.1654	-0.0004	-0.1175	0.2238	-0.0136	0.2612	0.3156	-0.0739	-0.0337	0.756	0.2243	0.3632	10.1005	33.8735	7.0835
4	1.8984	1.2907	-2.2912	0.8597	-1.6542	3.6912	-0.1243	0.2097	-0.0526	-0.1089	-0.1611	-0.1045	-0.0989	0.0548	0.0459	0.2684	-0.0844	-0.0267	0.8437	0.2384	0.3603	16.0843	40.6282	3.9468
5	0.9104	-0.3041	-0.3978	0.936	-0.3974	1.7773	0.0861	0.0045	-0.006	-0.0499	-0.083	-0.0543	-0.0134	0.0771	-0.0545	0.2447	-0.0461	-0.0257	0.7995	0.1624	0.2877	6.8709	44.9849	4.1377
6	0.6843	0.2483	-0.9204	0.2089	-0.3464	1.5816	-0.1182	0.0153	-0.0434	0.0194	0.094	-0.0252	0.1261	-0.1233	0.0093	0.2355	-0.0035	-0.0277	0.801	0.1932	0.3507	3.5045	38.1873	7.8816
7	0.653	0.0427	-0.0518	0.7934	-0.4349	1.1667	0.0126	0.0712	-0.1737	-0	0.0032	0.0236	-0.0459	-0.1481	-0.0142	0.2262	0.0052	-0.0789	0.9399	0.3207	0.124	-8.5657	29.6177	41.6182
8	3.6231	0.1022	0.3137	2.2385	3.1061	7.1831	0.0291	0.0789	0.0444	-0.1976	0.0133	0.069	-0.1347	-0.1773	0.0121	0.1238	-0.0893	0.0205	0.5739	0.1051	0.4494	-28.4846	-0.6101	33.096
9	2.6682	0.2667	1.647	3.1891	-1.5783	1.9787	-0.2913	0.1749	0.4498	-0.0527	0.0974	0.1253	-0.5785	-0.2223	0.1921	0.4751	0.0222	-0.048	1.1052	0.1438	0.4864	-48.9313	10.5488	-5.7287
10	0.8259	-0.4086	0.656	0.3035	-0.3714	1.2878	-0.0915	-0.0072	0.2929	-0.0576	-0.0489	0.0812	-0.0166	-0.2055	-0.0101	0.0923	-0.1241	0.0553	1.0521	0.25	0.2704	-43.9119	-1.3134	-6.2921
11	0.5007	-0.1269	0.791	0.162	-0.4853	1.6985	0.1276	0.0393	0.2171	0.079	0.1701	0.135	-0.3951	0.1816	0.0493	0.1976	0.0132	-0.1193	1.0305	0.3765	0.033	-36.9089	-0.0142	6.9237
12	0.8967	0.0862	0.3238	0.6621	0.1403	1.5516	0.0298	0.0703	0.0169	-0.0105	-0.0156	-0.1151	0.0757	0.1052	-0.0113	0.1876	0.0032	0.0028	0.6624	0.173	0.2437	-24.6494	-8.8499	30.6568
13	2.3157	-0.6374	-2.66	1.4807	2.6562	6.6676	-0.0001	-0.0886	-0.0421	0.1479	0.0407	0.0387	0.2702	-0.2012	-0.0067	0.116	0.0478	0.0211	0.5083	0.2238	0.5018	-6.8673	-40.6824	-14.6349
14	4.3632	-0.3176	-4.0474	2.2798	0.2402	3.7578	-0.3125	-0.092	-0.4188	-0.0694	0.1389	0.0143	0.5613	-0.234	0.1745	0.4217	-0.1124	0.0433	1.0507	0.1261	0.5851	-27.4024	-51.5935	24.4062
15	0.6353	0.0072	-0.4659	0.0906	-0.4655	1.4593	-0.0472	-0.0507	-0.1213	-0.0379	0.0524	0.0973	0.1737	-0.0827	-0.0148	0.1422	-0.0392	0.012	0.8752	0.205	0.3253	-18.153	-39.1784	17.1673
16	0.9698	-0.1272	-0.3278	0.4257	0.2727	1.32	0.0445	0.08	-0.1508	-0.0538	0.0649	-0.094	-0.0006	0.2353	-0.0606	0.2062	-0.0013	-0.0006	0.7168	0.1978	0.2917	-2.05	-33.7123	-14.6869
17	2.6383	-1.1294	1.7394	2.3943	1.0019	2.7431	-0.337	-0.4143	0.2058	0.3082	0.0311	-0.2553	-0.4995	0.2655	0.3542	0.4379	-0.0466	-0.037	0.9818	0.3152	0.4688	1.0644	3.9975	18.4176
18	0.5678	-0.1244	0.7775	0.4985	-0.2349	1.322	-0.0145	-0.115	0.1114	0.0107	0.0418	0.0359	-0.0601	0.1102	-0.0161	0.2038	0.0005	0.0014	0.7314	0.1736	0.3483	-5.2399	-5.674	11.6981
19	0.5893	-0.3172	0.5227	-0.0848	-0.4142	1.0826	-0.0193	-0.143	0.0014	-0.1096	0.0468	-0.1195	-0.1021	0.0989	0.0608	0.1958	-0.0411	-0.0358	0.8191	0.2431	0.3053	-9.687	-1.9897	2.5908
20	0.8611	-0.413	-0.2987	1.3072	-0.649	1.1488	0.2377	0.1185	0.2459	0.0383	0.1562	0.0711	0.1947	-0.1169	-0.1225	0.1246	-0.0345	0.1652	0.8719	0.3752	0.0476	-24.0807	7.0075	-24.9981
21	1.0588	0.1543	-0.289	1.0552	-0.6743	1.536	0.1779	0.0718	0.2191	-0.0816	0.0569	0.2072	-0.0592	-0.1018	-0.1349	0.1074	0.0025	0.0026	0.7422	0.1989	0.353	-24.8419	10.3429	-22.2429

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 1 through 14 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1 through 31 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 32 through 53 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 54 through 104 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 105 through 163 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 164 through 279 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 1 through 12 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 17 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 18 through 104 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 105 through 183 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 184 through 279 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 1 through 12 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 1 through 17 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 18 through 198 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 199 through 279 )
17	X-RAY DIFFRACTION	17	chain 'G' and (resid 1 through 17 )
18	X-RAY DIFFRACTION	18	chain 'G' and (resid 18 through 84 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 85 through 198 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 199 through 258 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 259 through 279 )

-
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://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