PDB-5cgb: Crystal structure of FimH in complex with heptyl alpha-D-septanoside

ID or keywords:

Entry

Database: PDB / ID: 5cgb

Title

Crystal structure of FimH in complex with heptyl alpha-D-septanoside

Components

Protein FimH

Keywords

SUGAR BINDING PROTEIN / UTI / lectin / urinary tract infection / type 1 fimbriae / pilus / inhibitor

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: 1.6 Å

Authors

Jakob, R.P. / Preston, R.P. / Zihlmann, P. / Fiege, B. / Sager, C.P. / Vannam, R. / Rabbani, S. / Zalewski, A. / Maier, T. / Ernst, B. / Peczuh, M.

Citation

Journal: Chem Sci / Year: 2018
Title: The price of flexibility - a case study on septanoses as pyranose mimetics.
Authors: Sager, C.P. / Fiege, B. / Zihlmann, P. / Vannam, R. / Rabbani, S. / Jakob, R.P. / Preston, R.C. / Zalewski, A. / Maier, T. / Peczuh, M.W. / Ernst, B.

History

Deposition	Jul 9, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 7, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cgb.cif.gz	195.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5cgb.ent.gz	158.7 KB	Display	PDB format
PDBx/mmJSON format	5cgb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cgb_validation.pdf.gz	719.5 KB	Display	wwPDB validaton report
Full document	5cgb_full_validation.pdf.gz	719.4 KB	Display
Data in XML	5cgb_validation.xml.gz	19.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cg/5cgb ftp://data.pdbj.org/pub/pdb/validation_reports/cg/5cgb	HTTPS FTP

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Related structure data

Related structure data	4lovS S: Starting model for refinement
Similar structure data	4av4-d 4xo8-1 6gtx-3 6g2s-3 5l4x-2 4x50-1 6gty-1 7ayn-1 1tr7-1 3mcy-3 7ayn-2 5muc-1 5fwr-7 6g2s-8 3zl2-d 7ayn-4 6g2s-1 4avk-2 5fwr-3 6gtx-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4lovS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein FimH

B: Protein FimH

hetero molecules

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

1

A: Protein FimH

hetero molecules

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

2

B: Protein FimH

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.580, 68.550, 95.780
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 K-12 (bacteria) / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli (E. coli) / Variant (production host): HM125 / References: UniProt: P08191
#2: Chemical	ChemComp-51C / (6R)-1,6-anhydro-2-O-heptyl-6-(hydroxymethyl)-D-galactitol Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₈O₆
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.12 % / Description: plates
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.5 M NH4SO4, 0.1 M BisTris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 17, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→47.89 Å / Num. obs: 55686 / % possible obs: 99.5 % / Redundancy: 8.1 % / R_merge(I) obs: 0.076 / Net I/σ(I): 19.7
Reflection shell	Resolution: 1.6→1.69 Å / Redundancy: 8 % / R_merge(I) obs: 0.76 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LOV

4lov

Resolution: 1.6→47.89 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1792	2760	4.96 %
R_work	0.16	-	-
obs	0.161	55686	99.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→47.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2392	0	50	475	2917

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2510
X-RAY DIFFRACTION	f_angle_d	1.166	3452
X-RAY DIFFRACTION	f_dihedral_angle_d	10.687	880
X-RAY DIFFRACTION	f_chiral_restr	0.053	406
X-RAY DIFFRACTION	f_plane_restr	0.005	440

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 (%)
1.5999-1.6275	0.2856	117	0.2616	2578	X-RAY DIFFRACTION	97
1.6275-1.6571	0.2419	141	0.2313	2585	X-RAY DIFFRACTION	99
1.6571-1.689	0.2478	115	0.2165	2627	X-RAY DIFFRACTION	100
1.689-1.7234	0.2207	134	0.1978	2628	X-RAY DIFFRACTION	99
1.7234-1.7609	0.2168	126	0.1819	2634	X-RAY DIFFRACTION	100
1.7609-1.8019	0.1955	154	0.1719	2593	X-RAY DIFFRACTION	99
1.8019-1.8469	0.186	136	0.169	2608	X-RAY DIFFRACTION	100
1.8469-1.8969	0.1844	135	0.1639	2617	X-RAY DIFFRACTION	100
1.8969-1.9527	0.1849	144	0.159	2628	X-RAY DIFFRACTION	99
1.9527-2.0157	0.1714	136	0.1589	2628	X-RAY DIFFRACTION	99
2.0157-2.0878	0.203	156	0.1487	2591	X-RAY DIFFRACTION	99
2.0878-2.1714	0.167	126	0.1416	2650	X-RAY DIFFRACTION	100
2.1714-2.2702	0.1649	131	0.1369	2663	X-RAY DIFFRACTION	100
2.2702-2.3899	0.1736	129	0.1332	2651	X-RAY DIFFRACTION	100
2.3899-2.5396	0.1679	157	0.1392	2647	X-RAY DIFFRACTION	100
2.5396-2.7357	0.1501	164	0.1429	2650	X-RAY DIFFRACTION	100
2.7357-3.0109	0.1827	135	0.1551	2668	X-RAY DIFFRACTION	100
3.0109-3.4465	0.1705	155	0.154	2686	X-RAY DIFFRACTION	100
3.4465-4.3418	0.1598	155	0.1523	2705	X-RAY DIFFRACTION	100
4.3418-47.9114	0.198	114	0.1799	2889	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	4.9755	1.2865	0.9875	6.6371	4.4508	3.0664	0.0631	-0.2815	0.5508	0.1742	-0.0421	-0.0913	-0.4362	0.2638	-0.0831	0.2167	-0.0335	0.0234	0.1869	-0.0118	0.151	-14.5925	0.0816	-2.6345
2	0.2988	0.4292	0.6856	2.2332	1.4251	4.9626	0.2276	-0.053	0.1454	0.0532	0.0439	-0.0224	-0.7013	0.0816	-0.2339	0.148	-0.0019	-0.0012	0.1579	0.001	0.1622	-14.3936	-0.8319	18.1835
3	0.2536	-0.1567	0.6696	0.8691	-1.6711	8.4584	0.0262	0.0142	0.035	0.0331	0.0957	0.0645	-0.304	0.1322	-0.1174	0.1697	-0.0002	0.0037	0.1541	-0.0047	0.1578	-23.0694	-1.2356	0.1758
4	8.3904	-0.6152	2.6675	1.2706	-0.7815	3.7324	0.2536	0.1311	-0.2975	-0.1067	-0.0083	0.0235	0.4842	0.2144	-0.2907	0.1371	-0.0056	0.0086	0.0759	-0.0175	0.0918	-19.0741	-12.419	3.9383
5	6.1988	1.3119	4.4575	1.3512	0.4694	3.2835	0.1343	-0.2914	-0.122	0.1103	-0.0389	-0.0323	0.1375	-0.1359	-0.0771	0.163	0.0045	-0.0021	0.1433	0.0051	0.134	-18.0708	-10.5497	18.3984
6	1.7257	-1.6659	1.548	3.7879	-4.1561	4.7386	0.0093	-0.0666	-0.1033	-0.1584	0.2509	0.2528	0.1392	-0.3704	-0.2922	0.1576	-0.017	-0.0108	0.1636	0.0079	0.1635	-25.6224	-12.8672	6.9658
7	0.9897	-0.8674	2.6964	0.9841	-2.537	8.6381	-0.0231	-0.0297	0.0838	0.0714	-0.0117	-0.0318	-0.0794	-0.0714	0.0345	0.1596	-0.007	0.0116	0.1484	0.0002	0.16	-22.3109	-4.2495	10.7299
8	6.0436	3.7094	-5.0023	3.1087	-3.2344	4.1594	-0.0616	-0.2397	-0.0269	0.1474	-0.1173	-0.2096	-0.0446	1.0428	0.1464	0.192	-0.0147	-0.0131	0.2274	-0.0012	0.1684	-6.9841	-3.4722	22.9333
9	6.5213	1.0903	7.2074	0.867	1.1586	8.6408	0.2858	0.0538	-0.1794	0.0052	-0.0204	-0.0285	0.4857	0.1259	-0.2535	0.1639	-0.0046	0.0031	0.1551	-0.0027	0.1277	-16.7651	-10.3053	2.6304
10	0.7666	0.2083	0.7783	0.7156	0.2458	3.9739	0.0153	0.0697	-0.0216	-0.0612	0.0361	-0.025	-0.0301	0.376	-0.0628	0.1617	0.0094	0.0194	0.1459	-0.0017	0.1456	-14.5689	-6.427	6.5585
11	5.2426	-0.0326	-0.1275	5.6451	-4.3983	3.5194	0.1896	-0.1952	-0.6595	0.1184	0.0587	0.3489	0.5027	-0.2623	-0.2126	0.2044	-0.0421	-0.012	0.1796	0.0106	0.1757	-48.9858	-0.0418	4.0425
12	0.2936	-0.1016	-0.2212	0.6608	-0.5327	5.8232	0.0346	-0.0182	-0.0529	-0.0061	-0.0009	0.0236	0.2816	0.0736	-0.0439	0.1837	-0.0185	0.0089	0.1565	0.0067	0.1708	-46.989	0.8788	23.8475
13	0.5538	-0.4199	-2.3615	1.0214	1.9041	7.6743	0.0711	0.038	0.0206	0.0019	0.0157	0.0055	-0.0708	-0.01	-0.0959	0.1098	0.0015	-0.0084	0.1647	-0.0019	0.1414	-42.9613	7.5946	11.038
14	0.489	-0.5001	-1.1117	1.1892	1.9133	5.2103	0.0274	-0.0259	0.0139	-0.0591	0.097	-0.0792	0.0269	0.3302	-0.1424	0.1124	-0.0061	0.0027	0.1759	-0.0182	0.1452	-39.7129	8.0838	15.7646
15	6.2714	3.6041	5.1195	2.6603	3.0039	4.17	-0.0982	-0.291	0.0758	0.0278	-0.0242	0.2614	-0.0862	-1.0241	0.1138	0.1244	0.0022	0.0123	0.1866	0.0056	0.1604	-56.6915	3.5716	29.5822
16	0.6981	0.0111	-1.5281	0.5732	-0.6567	5.7208	0.1329	0.0421	0.0647	-0.0099	0.0232	0.0204	-0.2518	-0.1307	-0.1518	0.131	-0.0163	-0.0025	0.1506	-0.0004	0.1333	-48.1507	7.7185	11.8824

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 64 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 65 through 77 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 78 through 95 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 96 through 116 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 117 through 124 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 125 through 135 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 136 through 158 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 15 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 16 through 40 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 41 through 77 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 78 through 116 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 117 through 124 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 125 through 158 )

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