PDB-5lng: Lectin domain of E. coli F9 pilus adhesin FmlH

ID or keywords:

Entry

Database: PDB / ID: 5lng

Title

Lectin domain of E. coli F9 pilus adhesin FmlH

Components

Putative Fml fimbrial adhesin FmlD

Keywords

CELL ADHESION / fimbrial adhesin / lectin / O-glycan

Function / homology

Function and homology information

cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Ruer, S. / Conover, M.S. / Kalas, V. / Taganna, J. / De Greve, H. / Pinkner, J.S. / Dodson, K.W. / Hultgren, S.J. / Remaut, H.

Funding support

Belgium,

United States, 2items

Citation

Journal: Cell Host Microbe / Year: 2016
Title: Inflammation-Induced Adhesin-Receptor Interaction Provides a Fitness Advantage to Uropathogenic E. coli during Chronic Infection.
Authors: Conover, M.S. / Ruer, S. / Taganna, J. / Kalas, V. / De Greve, H. / Pinkner, J.S. / Dodson, K.W. / Remaut, H. / Hultgren, S.J.

History

Deposition	Aug 4, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2016	Group: Database references
Revision 2.0	Jan 31, 2018	Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lng.cif.gz	248.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5lng.ent.gz	201.3 KB	Display	PDB format
PDBx/mmJSON format	5lng.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ln/5lng ftp://data.pdbj.org/pub/pdb/validation_reports/ln/5lng	HTTPS FTP

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Related structure data

Related structure data	5lneC C: citing same article (ref.)
Similar structure data	6aro-2 6aow-2 6arn-2 6aoy-1 2guz-7 6aow-1 2guz-4 3zpd-d 4b9g-1 6arm-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

5lneC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative Fml fimbrial adhesin FmlD

B: Putative Fml fimbrial adhesin FmlD

C: Putative Fml fimbrial adhesin FmlD

D: Putative Fml fimbrial adhesin FmlD

hetero molecules

72.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative Fml fimbrial adhesin FmlD

hetero molecules

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

2

B: Putative Fml fimbrial adhesin FmlD

hetero molecules

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

3

C: Putative Fml fimbrial adhesin FmlD

hetero molecules

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

4

D: Putative Fml fimbrial adhesin FmlD

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.710, 52.730, 62.820
Angle α, β, γ (deg.)	66.90, 82.28, 84.10
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	A	A	1 - 157	1 - 157
2	1	PRO	PRO	B	B	1 - 157	1 - 157
1	2	MET	MET	A	A	1 - 156	1 - 156
2	2	MET	MET	C	C	1 - 156	1 - 156
1	3	VAL	VAL	A	A	1 - 155	1 - 155
2	3	VAL	VAL	D	D	1 - 155	1 - 155
1	4	MET	MET	B	B	1 - 156	1 - 156
2	4	MET	MET	C	C	1 - 156	1 - 156
1	5	MET	MET	B	B	1 - 156	1 - 156
2	5	MET	MET	D	D	1 - 156	1 - 156
1	6	MET	MET	C	C	1 - 156	1 - 156
2	6	MET	MET	D	D	1 - 156	1 - 156

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Putative Fml fimbrial adhesin FmlD / FmlH Mass: 17805.984 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fmlD, UTI89_C1716 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q1RBS0, UniProt: A0A0H2V7F6*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.23 Å³/Da / Density % sol: 44.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Citrate pH2, 1M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.09→58 Å / Num. all: 95705 / Num. obs: 35660 / % possible obs: 97.8 % / Redundancy: 2.7 % / B_iso Wilson estimate: 36 Å² / R_merge(I) obs: 0.073 / Net I/σ(I): 8
Reflection shell	Resolution: 2.09→2.14 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.547 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
XDS		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.09→57.48 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.927 / SU B: 11.961 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23854	1785	5 %	RANDOM
R_work	0.19715	-	-	-
obs	0.19924	33875	97.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 43.827 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.21 Å²	1.34 Å²	0.29 Å²
2-	-	0.58 Å²	-1.31 Å²
3-	-	-	0.64 Å²

Refinement step

Cycle: 1 / Resolution: 2.09→57.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4613	0	50	204	4867

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.02	4784
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	4397
X-RAY DIFFRACTION	r_angle_refined_deg	1.846	1.944	6553
X-RAY DIFFRACTION	r_angle_other_deg	1.364	3	10097
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.783	5	594
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.215	25.204	196
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.597	15	702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.832	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	751
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	5410
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1095
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.629	2.557	2400
X-RAY DIFFRACTION	r_mcbond_other	1.627	2.556	2399
X-RAY DIFFRACTION	r_mcangle_it	2.465	3.821	2983
X-RAY DIFFRACTION	r_mcangle_other	2.465	3.821	2984
X-RAY DIFFRACTION	r_scbond_it	2.134	2.829	2384
X-RAY DIFFRACTION	r_scbond_other	1.938	2.758	2345
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.098	4.058	3510
X-RAY DIFFRACTION	r_long_range_B_refined	5.639	21.317	5069
X-RAY DIFFRACTION	r_long_range_B_other	5.495	21.114	5017
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	17528	0.06
1	2	B	17528	0.06
2	1	A	16926	0.05
2	2	C	16926	0.05
3	1	A	17466	0.05
3	2	D	17466	0.05
4	1	B	16962	0.05
4	2	C	16962	0.05
5	1	B	17552	0.05
5	2	D	17552	0.05
6	1	C	17018	0.05
6	2	D	17018	0.05

LS refinement shell

Resolution: 2.09→2.144 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	117	-
R_work	0.285	2476	-
obs	-	-	96.79 %

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	2.5196	-1.0492	1.1766	3.4161	-0.6552	0.5988	0.2283	0.0234	-0.2616	0.0349	-0.1515	-0.227	0.1825	0.0328	-0.0768	0.2108	-0.0067	0.0443	0.0905	-0.0496	0.1584	0.639	21.495	18.484
2	8.1055	0.4843	0.2972	2.6469	-0.9142	3.4447	0.0669	0.1463	0.2702	0.002	0.0552	0.3181	0.0025	-0.6589	-0.122	0.0925	0.0137	-0.0139	0.1986	-0.0466	0.1082	-13.082	32.494	6.788
3	4.0139	0.2194	-0.5777	2.9863	-0.332	2.6069	0.0538	0.2986	-0.3712	-0.0044	-0.057	-0.1852	0.2292	0.0819	0.0032	0.1409	-0.0014	-0.0001	0.0539	-0.0585	0.088	3.604	26.502	9.317
4	5.7237	-2.2608	1.9597	4.8284	-2.2305	3.5366	0.0563	0.0777	-0.1307	0.2124	-0.1233	-0.083	-0.0582	0.1092	0.067	0.0914	-0.0432	0.0347	0.0419	-0.0435	0.0662	2.548	29.351	17.66
5	3.383	-0.7136	0.452	1.2832	-0.9709	1.0312	-0.1252	0.2911	0.4526	-0.024	0.1669	0.2943	-0.0421	-0.2094	-0.0417	0.1002	-0.0469	-0.0425	0.2041	0.0197	0.3537	10.082	11.178	-17.157
6	2.7688	1.4198	0.2364	6.9384	-1.6255	3.0643	0.0099	0.1577	-0.3547	0.1254	-0.0052	-0.0428	0.5042	0.0218	-0.0047	0.1628	0.0032	0.072	0.0664	-0.0266	0.1219	19.972	-3.965	-5.482
7	2.9189	0.4903	-0.1583	3.2061	0.4472	1.8213	-0.0925	0.0647	0.3246	0.1669	0.1347	0.5206	-0.0317	-0.2541	-0.0422	0.0421	-0.0075	0.0497	0.1119	0.0025	0.167	15.618	13.033	-7.906
8	4.2097	-2.4686	1.7406	5.5796	-1.8413	2.8076	-0.0705	0.3352	0.1973	-0.1565	0.0059	0.3217	-0.0302	0.0784	0.0647	0.0325	-0.0529	-0.0004	0.1066	-0.0164	0.1428	18.708	11.661	-16.452
9	3.1016	-0.5968	-1.0447	2.7635	0.0751	0.6938	0.2954	-0.2748	0.707	0.2274	-0.2039	0.4221	-0.1653	0.053	-0.0915	0.2728	-0.0687	0.0579	0.0728	-0.163	0.4706	4.175	3.8	18.794
10	8.5835	1.1063	-0.6102	2.7229	0.4174	1.8265	0.0849	0.1153	-0.1349	0.0569	0.0032	-0.3246	0.0465	0.4854	-0.0881	0.1163	0.0053	-0.0059	0.1841	0.0235	0.1301	16.989	-6.824	6.99
11	5.171	0.6503	0.5032	2.821	-0.3311	1.8094	0.047	0.1307	0.8395	0.0431	-0.0822	0.3883	-0.2304	-0.0979	0.0351	0.1347	0.0039	0.0049	0.0177	0.0095	0.2242	0.027	-0.647	9.293
12	6.0388	-1.4461	-1.9969	4.9994	1.8516	3.2641	0.1105	-0.4487	0.4468	0.2883	-0.1306	0.3883	0.0278	0.1156	0.0201	0.1337	-0.0583	0.0168	0.0592	-0.0643	0.1573	1.949	-4.143	17.773
13	3.4598	-1.5513	-0.8331	3.3005	1.0078	0.6326	-0.233	0.0254	-0.0967	0.1613	0.2364	-0.3432	0.0853	0.1102	-0.0034	0.0826	-0.0419	-0.017	0.1184	-0.0361	0.1006	-6.134	14.546	-16.802
14	2.2215	1.1887	-0.1486	8.8668	0.0566	3.4946	0.0871	-0.0449	0.3312	0.1615	-0.079	-0.0996	-0.7595	-0.009	-0.008	0.1779	0.0115	-0.0129	0.0766	-0.0741	0.1297	-16.124	30.14	-5.374
15	3.2045	-0.0266	-0.2202	3.5843	-0.8357	2.081	-0.1356	-0.0685	-0.1983	0.1623	0.1891	-0.3558	0.0708	0.2108	-0.0535	0.0475	0.0009	-0.0254	0.1058	-0.0532	0.0801	-11.797	12.213	-7.665
16	4.1878	-2.1983	-2.0534	4.9264	1.8181	3.2084	-0.2319	0.2003	-0.1626	-0.0127	0.1222	0.0522	0.156	-0.078	0.1096	0.0506	-0.0447	-0.0044	0.0619	-0.0153	0.0327	-13.849	12.913	-16.486

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 43
2	X-RAY DIFFRACTION	2	A	44 - 57
3	X-RAY DIFFRACTION	3	A	58 - 109
4	X-RAY DIFFRACTION	4	A	110 - 157
5	X-RAY DIFFRACTION	5	B	1 - 43
6	X-RAY DIFFRACTION	6	B	44 - 57
7	X-RAY DIFFRACTION	7	B	58 - 109
8	X-RAY DIFFRACTION	8	B	110 - 157
9	X-RAY DIFFRACTION	9	C	1 - 43
10	X-RAY DIFFRACTION	10	C	44 - 57
11	X-RAY DIFFRACTION	11	C	58 - 109
12	X-RAY DIFFRACTION	12	C	117 - 156
13	X-RAY DIFFRACTION	13	D	1 - 43
14	X-RAY DIFFRACTION	14	D	44 - 57
15	X-RAY DIFFRACTION	15	D	58 - 109
16	X-RAY DIFFRACTION	16	D	110 - 156

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