PDB-6g2r: Crystal structure of FimH in complex with a tetraflourinated biph...

ID or keywords:

Entry

Database: PDB / ID: 6g2r

Title

Crystal structure of FimH in complex with a tetraflourinated biphenyl alpha D-mannoside

Components

Type 1 fimbrin D-mannose specific adhesin

Keywords

CELL ADHESION / TYPE I PILUS / CATCH-BOND / LECTIN / UPEC / INFECTION / MANNOSE

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: 2.1 Å

Authors

Jakob, R.P. / Schoenemann, W. / Cramer, J. / Muehlethaler, T. / Daetwyler, P. / Zihlmann, P. / Fiege, B. / Sager, C.P. / Smiesko, M. / Rabbani, S. ...

Citation

Journal: Chemmedchem / Year: 2019
Title: Improvement of Aglycone pi-Stacking Yields Nanomolar to Sub-nanomolar FimH Antagonists.
Authors: Schonemann, W. / Cramer, J. / Muhlethaler, T. / Fiege, B. / Silbermann, M. / Rabbani, S. / Datwyler, P. / Zihlmann, P. / Jakob, R.P. / Sager, C.P. / Smiesko, M. / Schwardt, O. / Maier, T. / Ernst, B.

History

Deposition	Mar 23, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 17, 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 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6g2r.cif.gz	192.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6g2r.ent.gz	156.5 KB	Display	PDB format
PDBx/mmJSON format	6g2r.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6g2r_validation.pdf.gz	943.6 KB	Display	wwPDB validaton report
Full document	6g2r_full_validation.pdf.gz	944.5 KB	Display
Data in XML	6g2r_validation.xml.gz	16.4 KB	Display
Data in CIF	6g2r_validation.cif.gz	23.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g2/6g2r ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g2r	HTTPS FTP

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Related structure data

Related structure data	6g2sC 4x50S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cgb-2 6g2s-5 3mcy-4 5jcr-2 4cst-d 7ayn-2 4x5q-d 5fs5-d 4xo8-2 4av5-2 5mts-1 3mcy-3 5l4w-1 3zl1-1 6gty-5 7ayn-4 5fwr-5 7ayn-1 5l4y-2 5mts-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

6g2sC

4x50S

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: Type 1 fimbrin D-mannose specific adhesin

B: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

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

1

A: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

defined by author
Evidence: gel filtration
17.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type 1 fimbrin D-mannose specific adhesin

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.115, 60.800, 105.938
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Type 1 fimbrin D-mannose specific adhesin / 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) Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli (E. coli) / Strain (production host): HM125 / References: UniProt: P08191
#2: Chemical	ChemComp-EJK / 4-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]-2,3,5,6-tetrakis(fluoranyl)benzenecarbonitrile Mass: 463.764 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₁₄ClF₄NO₆
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Details: From gel filtration buffer / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.58 Å³/Da / Density % sol: 52.24 % / Description: t
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaAcetate pH 5.0, 1.5 M NH4sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.87287 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.87287 Å / Relative weight: 1
Reflection	Resolution: 2.1→52.969 Å / Num. obs: 20986 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC_1/2: 0.994 / R_rim(I) all: 0.152 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2067 / CC_1/2: 0.479 / R_rim(I) all: 1.9 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.12rc1_2801: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4X50

4x50

Resolution: 2.1→52.969 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.29

	R_factor	Num. reflection	% reflection
R_free	0.2215	1653	7.88 %
R_work	0.1946	-	-
obs	0.1967	20986	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→52.969 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2392	0	82	242	2716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2539
X-RAY DIFFRACTION	f_angle_d	0.842	3500
X-RAY DIFFRACTION	f_dihedral_angle_d	11.734	1459
X-RAY DIFFRACTION	f_chiral_restr	0.052	404
X-RAY DIFFRACTION	f_plane_restr	0.005	442

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 (%)
2.1-2.1618	0.2699	134	0.2428	1574	X-RAY DIFFRACTION	99
2.1618-2.2316	0.3077	136	0.2401	1578	X-RAY DIFFRACTION	100
2.2316-2.3113	0.2782	136	0.2281	1581	X-RAY DIFFRACTION	100
2.3113-2.4039	0.2551	135	0.2309	1574	X-RAY DIFFRACTION	99
2.4039-2.5133	0.2507	136	0.2277	1590	X-RAY DIFFRACTION	100
2.5133-2.6458	0.231	137	0.2236	1598	X-RAY DIFFRACTION	99
2.6458-2.8115	0.2428	135	0.2165	1592	X-RAY DIFFRACTION	100
2.8115-3.0286	0.2092	139	0.2032	1629	X-RAY DIFFRACTION	100
3.0286-3.3333	0.2078	137	0.1829	1595	X-RAY DIFFRACTION	100
3.3333-3.8156	0.2037	140	0.1655	1636	X-RAY DIFFRACTION	100
3.8156-4.8067	0.16	140	0.1461	1646	X-RAY DIFFRACTION	100
4.8067-52.9858	0.2454	148	0.2081	1740	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	8.5774	-4.5106	1.0222	2.5702	-1.0401	4.4925	0.1785	-0.578	-0.5627	0.7827	0.1385	0.1526	0.288	-0.1937	-0.1946	0.3385	-0.0189	-0.0482	0.2893	-0.0478	0.2993	17.0477	0.4686	7.2404
2	8.4039	-6.656	-3.6871	8.4588	1.3298	2.7322	-0.6004	-0.511	-0.3578	0.9754	0.2823	-0.0617	0.6042	0.1176	0.4981	0.1903	-0.0418	-0.044	0.2681	0.0441	0.2836	32.6374	-10.024	-1.3509
3	8.8919	-4.7593	-2.3295	4.8274	3.0409	8.617	-0.0693	0.359	-1.1761	0.2134	-0.4286	0.5351	-0.0085	-0.0427	0.4052	0.2429	0.0096	0.0366	0.2533	-0.0131	0.4097	26.3043	-11.3339	-4.4086
4	6.6473	-1.6938	-1.2852	2.2894	0.2917	2.2534	0.1314	-0.0983	-0.0597	0.0255	-0.0347	0.1111	-0.0188	0.1012	-0.1088	0.2112	-0.0088	-0.0146	0.1658	-0.0198	0.2494	19.4197	-0.6973	-4.4086
5	9.0296	-2.9651	-2.0532	1.4583	1.0764	3.7108	0.2008	0.6331	-0.0958	-0.2197	-0.2812	-0.1543	-0.112	-0.1218	0.024	0.2381	0.023	0.002	0.2665	0.0096	0.262	19.0327	-1.0862	-12.0592
6	3.6617	-1.7637	-5.1151	2.2443	2.3867	7.1515	0.0921	-0.4567	-0.4539	0.0611	-0.0549	0.3083	-0.0278	0.0514	-0.0475	0.1814	0	0.0217	0.1636	0.0641	0.3144	18.1191	-6.9399	-3.4807
7	6.182	-3.087	-1.07	3.4312	0.8152	1.2271	-0.0752	-0.0858	0.1737	0.0355	0.1176	-0.2445	-0.055	0.0884	-0.1834	0.1685	-0.0289	0.0302	0.1995	-0.0085	0.2118	31.4545	-2.0997	-3.8438
8	6.644	-2.7281	-1.2984	3.9826	0.4509	2.1029	-0.2707	-0.621	0.2807	0.2358	0.3799	-0.1743	-0.0796	0.2094	-0.0322	0.1618	-0.0348	0.0252	0.1502	0.0033	0.1259	24.7545	-0.1764	-0.9286
9	6.8641	1.0886	-1.8428	3.7174	2.1317	5.1369	-0.2278	-0.4298	-0.5465	0.4984	0.1491	-0.3749	1.2863	0.4407	-0.0038	0.468	0.0092	0.0235	0.151	0.0159	0.3194	-8.0068	3.5594	20.6162
10	3.5053	1.5755	-2.5628	1.3233	-1.3113	4.5587	-0.0662	-0.2208	0.0109	0.0109	-0.0389	-0.021	0.2181	0.1562	0.0828	0.1969	0.0161	-0.031	0.1749	0.0345	0.2914	-13.1108	9.1549	28.9815
11	7.759	2.9433	-4.124	1.5716	-2.1294	3.9972	-0.1141	0.4645	0.0664	-0.0926	0.2756	0.1168	0.0028	-0.7886	-0.1431	0.2352	0.0395	-0.0317	0.3523	0.0084	0.298	-22.6494	13.5905	25.4299
12	7.9339	1.3529	-3.6876	1.8965	-1.0484	3.8159	0.1769	0.462	0.953	-0.1776	0.1594	0.448	-0.562	-0.7549	-0.3994	0.3061	0.0961	0.009	0.4059	0.0543	0.3357	-17.6456	20.1361	23.2046
13	7.6319	0.61	-6.1292	1.4507	-0.8972	6.3386	-0.1018	-0.4639	0.261	0.0553	0.0541	-0.141	-0.1391	0.4324	-0.0195	0.2111	0.0109	-0.0468	0.2156	0.0044	0.3036	-11.5076	13.5591	28.2731
14	6.0634	-1.4318	-3.096	4.7407	-1.6409	4.7008	-0.3022	0.3061	-0.6236	0.0677	-0.0601	1.5357	0.2436	-0.7948	0.2594	0.2134	-0.1098	-0.0279	0.4377	-0.0128	0.5132	-32.4645	4.2642	36.7292
15	3.3059	3.5423	-0.7635	5.6303	-3.3969	3.64	-0.0463	0.3673	0.3994	-0.1814	0.184	0.4456	0.1524	-0.5952	-0.3426	0.1732	0.0037	-0.0171	0.2438	-0.0185	0.255	-16.8193	11.0275	19.164
16	5.0403	3.7205	-5.1387	3.6332	-5.1301	8.9765	-0.343	0.3715	-0.0199	-0.3912	0.2241	0.1445	0.6305	-0.5842	0.0842	0.2604	-0.0192	0.0116	0.2279	-0.0315	0.2149	-12.9656	9.5917	15.743
17	8.2053	-1.1049	-4.2333	7.8368	-0.6246	9.026	-0.1	-0.5876	-0.5358	0.4295	0.0073	0.4109	-0.2365	-0.6	0.1349	0.2395	-0.0481	-0.0536	0.3904	-0.017	0.3523	-28.4154	3.0736	41.7577

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 40 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 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 135 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 136 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 53 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 54 through 77 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 78 through 95 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 96 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 135 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 136 through 150 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 151 through 158 )

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