PDB-4xob: Crystal structure of a FimH*DsF complex from E.coli K12 with boun...

ID or keywords:

Entry

Database: PDB / ID: 4xob

Title

Crystal structure of a FimH*DsF complex from E.coli K12 with bound heptyl alpha-D-mannopyrannoside

Components

FimF
Protein FimH

Keywords

CELL ADHESION / foldase / prolyl isomerase / protein secretion / Gram-positive / isomerase

Function / homology

Function and homology information

pilus assembly / 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: 3.003 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
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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Download

PDBx/mmCIF format	4xob.cif.gz	629.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4xob.ent.gz	537.3 KB	Display	PDB format
PDBx/mmJSON format	4xob.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xob_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4xob_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4xob_validation.xml.gz	40.8 KB	Display
Data in CIF	4xob_validation.cif.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xo/4xob ftp://data.pdbj.org/pub/pdb/validation_reports/xo/4xob	HTTPS FTP

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Related structure data

Related structure data	4xo8C 4xo9C 4xoaC 4xocC 4xodC 4xoeC 1qunS 3mcyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gtz-2 6gtz-1 5jqi-4 6gtv-1 6gtv-2 5jqi-3 5jqi-2 4xo9-d 2j3s-2 4xoe-d 1139 5jqi-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein FimH

B: FimF

C: Protein FimH

D: FimF

E: Protein FimH

F: FimF

G: Protein FimH

H: FimF

hetero molecules

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

1

A: Protein FimH

B: FimF

hetero molecules

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

2

C: Protein FimH

D: FimF

hetero molecules

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

3

E: Protein FimH

F: FimF

hetero molecules

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

4

G: Protein FimH

H: FimF

hetero molecules

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

Unit cell

Length a, b, c (Å)	94.469, 147.128, 250.796
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	24
Space group name H-M	I2₁2₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-408- HOH
2	1	G-602- HOH

#1: 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) / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#2: Protein/peptide	FimF / Fimbrial protein Mass: 1639.768 Da / Num. of mol.: 4 / Fragment: UNP residues 23-37 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimF, EcDH1_3679, ECDH1ME8569_4176 / Plasmid: pTRC / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: C9QSZ9, UniProt: P08189*PLUS
#3: 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.: 4 / Source method: obtained synthetically / Formula: C₁₃H₂₆O₆ / Comment: detergent*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 65.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30 % w/v PEG 5,000, 0.1 M MES monohydrate, 0.2 M Ammonium sulfate pH 6.5. 2.5fold excess ligand to protein

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99998 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99998 Å / Relative weight: 1
Reflection	Resolution: 3.003→48.131 Å / Num. obs: 35265 / % possible obs: 99.8 % / Redundancy: 6.6 % / R_merge(I) obs: 0.425 / Net I/σ(I): 14.3
Reflection shell	Resolution: 3.003→3.18 Å / Redundancy: 4.1 % / R_merge(I) obs: 2.073 / Mean I/σ(I) obs: 1.5 / Num. unique all: 5614 / % possible all: 97.4

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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: 3.003→48.131 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2454	1764	5 %
R_work	0.2265	-	-
obs	0.2275	35265	99.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.003→48.131 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8616	0	86	119	8821

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8928
X-RAY DIFFRACTION	f_angle_d	0.999	12251
X-RAY DIFFRACTION	f_dihedral_angle_d	11.309	3059
X-RAY DIFFRACTION	f_chiral_restr	0.041	1474
X-RAY DIFFRACTION	f_plane_restr	0.005	1581

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 (%)
3.003-3.0841	0.3757	130	0.3534	2481	X-RAY DIFFRACTION	98
3.0841-3.1749	0.3025	135	0.3014	2552	X-RAY DIFFRACTION	100
3.1749-3.2773	0.3172	134	0.2932	2538	X-RAY DIFFRACTION	100
3.2773-3.3944	0.2872	135	0.2812	2565	X-RAY DIFFRACTION	100
3.3944-3.5303	0.2959	133	0.2632	2537	X-RAY DIFFRACTION	100
3.5303-3.6909	0.2999	136	0.2712	2576	X-RAY DIFFRACTION	100
3.6909-3.8854	0.2591	134	0.246	2547	X-RAY DIFFRACTION	100
3.8854-4.1287	0.2477	136	0.2199	2588	X-RAY DIFFRACTION	100
4.1287-4.4473	0.2212	134	0.1851	2557	X-RAY DIFFRACTION	100
4.4473-4.8945	0.1698	137	0.1657	2588	X-RAY DIFFRACTION	100
4.8945-5.6018	0.1872	137	0.1713	2606	X-RAY DIFFRACTION	100
5.6018-7.0541	0.2181	138	0.213	2620	X-RAY DIFFRACTION	100
7.0541-48.1372	0.2454	145	0.2153	2746	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	3.8265	2.8477	-0.8505	3.5688	-0.2441	1.4491	0.1649	-0.0057	0.1041	0.0033	-0.1497	-0.1017	-0.2665	-0.0227	-0.0596	0.2886	0.0251	-0.0038	0.1637	0.0344	0.2538	1.7452	48.6677	13.4727
2	4.9808	2.3066	-0.6871	3.7715	0.1783	2.6937	-0.0396	0.0108	0.2196	-0.2422	0.0194	-0.1803	-0.0003	0.1318	0.0807	0.2985	0.0287	0.0389	0.1604	-0.0287	0.2666	1.7723	51.5712	13.9203
3	1.9057	0.72	0.8115	1.3941	1.1246	1.2319	0.1049	0.0143	0.0083	0.0871	-0.0509	0.0664	0.1265	-0.133	-0.0903	0.2337	0.0025	-0.0192	0.2251	0.0643	0.2434	-30.1355	26.7483	22.3106
4	3.4791	1.8062	2.4079	4.6146	2.8335	2.4207	-0.3058	0.3088	-0.175	-0.7365	0.1064	0.0283	-0.3473	0.0534	0.1708	0.3719	-0.0045	0.1156	0.4815	0.0207	0.3022	-34.3108	23.7475	13.052
5	3.1546	0.2117	2.6981	1.7374	0.8569	7.4088	0.601	-0.3874	-0.2916	0.694	-0.097	0.6636	0.4111	-0.9016	-0.0735	0.646	-0.0718	-0.0827	0.4633	0.2222	0.5017	-17.4073	15.5479	77.4122
6	0.7073	0.1001	-0.1155	2.2293	0.9508	3.7767	0.0444	-0.0792	-0.1414	0.2616	-0.0169	0.5148	-0.0098	-0.5448	-0.0901	0.3862	0.07	-0.0102	0.4079	0.1548	0.3914	-14.7624	19.6783	67.459
7	3.8707	-2.1076	-1.9113	4.5365	1.7511	3.0787	-0.4362	-0.0181	-0.207	0.3481	0.0353	0.0567	0.096	1.2596	0.3842	0.4036	0.0714	-0.1216	0.4812	0.091	0.4179	-3.5315	19.941	65.9507
8	0.8451	1.8988	0.2513	2.4966	0.0505	4.8549	-0.0669	0.1418	0.3165	0.2335	-0.0718	-0.065	-0.3753	0.1414	0.1854	0.3076	0.0722	-0.0134	0.3786	0.1034	0.3447	-8.1953	24.3169	65.7204
9	0.5529	-0.0581	-0.3256	0.8326	-0.1476	3.8499	-0.089	0.0074	-0.0714	-0.0766	-0.0001	-0.0746	0.4728	-0.0493	0.0733	0.3967	0.0208	-0.0307	0.2439	0.0853	0.3452	-8.1669	7.9877	43.8109
10	2.12	0.0996	0.1165	3.4574	0.6002	3.3013	0.2334	0.4135	-0.298	0.1096	-0.2288	-0.5395	1.0749	-0.2098	0.0142	0.7881	-0.0079	0.1188	0.496	0.1275	0.3538	-7.0711	-2.6208	28.2333
11	2.8279	1.8422	1.8489	5.092	3.109	3.7648	0.201	0.0885	-0.5846	-0.777	0.1536	-0.4097	0.3622	-0.4124	-0.3347	0.8529	-0.0901	0.0375	0.3847	0.0533	0.4095	-12.8825	-6.1622	31.9617
12	6.1617	2.2409	1.2298	7.0279	-2.707	2.5587	-0.277	-0.2912	0.3172	-0.4771	0.4005	0.3767	0.9463	-1.4476	-0.4042	0.232	-0.3215	-0.0711	0.8217	0.256	0.482	-31.2357	6.9444	52.1202
13	1.9084	0.6386	0.5374	2.6583	1.8999	4.4544	-0.1708	0.1744	0.0497	-0.1429	0.1994	0.2308	0.1688	0.2258	-0.0448	0.2212	-0.0453	-0.0507	0.396	0.1008	0.2936	-25.8227	19.8175	48.2799
14	3.0708	0.7639	0.9098	0.0823	0.0956	3.4385	0.3213	0.2363	-0.1715	0.2454	-0.2966	-0.9389	0.2859	0.123	-0.0258	0.2342	0.0038	-0.0781	0.3628	0.152	0.3923	-22.2013	20.9455	51.2251
15	1.1863	-0.0416	0.0616	2.0669	-0.2573	1.7367	-0.0383	0.0968	-0.1128	-0.148	0.2525	0.5457	0.1945	-0.2346	-0.0697	0.2754	-0.0902	-0.0605	0.3886	0.1392	0.4017	-32.9435	16.3376	48.6452
16	1.5837	-0.3261	-0.1401	3.1697	1.0479	1.8952	-0.0215	-0.477	0.2081	0.6551	0.2969	-0.067	-0.0865	-0.236	-0.2905	0.4928	0.0811	-0.0645	0.4024	-0.0022	0.4543	-21.939	36.9064	75.4176
17	3.4262	-1.3538	-0.1145	2.9177	1.4896	4.9127	-0.3433	-0.5355	0.5163	0.7117	0.4213	0.2332	-0.1198	-0.0473	-0.1373	0.4485	0.1482	-0.019	0.4105	-0.013	0.6097	-21.7711	47.584	77.3243
18	2.9887	-0.0272	-0.5091	3.3047	1.1769	6.115	-0.1727	-0.5469	0.6141	0.7432	0.2942	-0.1629	-0.3201	0.1501	-0.1468	0.4905	0.1368	-0.1046	0.4289	-0.1146	0.5698	-18.4359	49.523	78.5629
19	2.6561	0.173	-1.8552	2.5084	-0.9699	7.2475	0.7669	-0.5097	0.0472	0.7083	0.9333	0.776	-0.962	-0.8135	-0.9442	0.5773	0.1055	0.1037	0.4014	0.0282	0.6723	-24.3094	42.8217	86.6075
20	7.4633	2.088	-1.5598	4.9085	-2.5023	4.1403	0.5112	-1.0652	0.0887	0.2469	-0.9992	-0.1845	-0.4478	1.0173	0.3036	0.5725	-0.1512	0.1313	0.5915	0.1008	0.4081	-51.4052	11.4843	67.8321
21	0.55	-0.2184	-2.1023	-0.9542	1.2327	1.212	-0.3745	0.3465	0.0263	0.0476	0.0236	0.2524	0.2933	-0.4289	0.3316	0.9799	-0.1903	0.2103	0.6878	0.0015	0.9674	-63.844	8.4362	43.6497
22	3.1483	-0.0978	-1.589	4.0144	0.1694	3.9121	0.0362	0.156	-0.013	1.1143	0.0452	0.9575	0.4793	-1.1204	-0.1047	0.6697	-0.259	0.131	0.7174	0.0944	0.6244	-58.7393	13.7675	31.7979
23	6.0836	-2.0497	-2.1108	6.41	0.6655	4.574	0.8637	0.1395	0.0857	1.1966	0.3745	0.6429	0.2607	0.1514	-0.4993	0.7719	-0.3701	0.4532	0.3933	0.4593	0.6032	-51.4473	4.9562	33.4689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 84 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 85 through 150 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 151 through 279 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 14 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 15 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 16 through 53 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 54 through 77 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 78 through 116 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 117 through 252 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 253 through 279 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 14 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 1 through 15 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 16 through 95 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 96 through 116 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 117 through 150 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 151 through 177 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 178 through 220 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 221 through 279 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 2 through 14 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 1 through 150 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 151 through 177 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 178 through 279 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 2 through 14 )

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