PDB-5afo: Long Polar Fimbriae adhesin LpfD from the adherent invasive E. co...

ID or keywords:

Entry

Database: PDB / ID: 5afo

Title

Long Polar Fimbriae adhesin LpfD from the adherent invasive E. coli strain LF82

Components

FIMBRIAE

Keywords

CELL ADHESION / LONG POLAR FIMBRIAE / AIEC / CROHN'S DISEASE / ADHESIN / PILI

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 / OTHER / Resolution: 1.82 Å

Authors

Coppens, F. / Iyyathurai, J. / Remaut, H.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and Adhesive Properties of the Long Polar Fimbriae Protein Lpfd from Adherent-Invasive Escherichia Coli.
Authors: Coppens, F. / Iyyathurai, J. / Ruer, S. / Fioravanti, A. / Taganna, J. / Vereecke, L. / De Greve, H. / Remaut, H.

History

Deposition	Jan 23, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2015	Group: Database references
Revision 1.2	Aug 19, 2015	Group: Database references
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5afo.cif.gz	289.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5afo.ent.gz	240.1 KB	Display	PDB format
PDBx/mmJSON format	5afo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	5cyl-1 5cyl-5 5cyl-2 5fn6-d 5cyl-8 5dns-1 5cyl-4 2v05-d 5cyl-6 5cyl-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: FIMBRIAE

B: FIMBRIAE

hetero molecules

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

1

A: FIMBRIAE

hetero molecules

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

2

B: FIMBRIAE

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.010, 372.130, 99.030
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (-0.975, 0.003, 0.22), (0.001, -1, 0.015), (0.22, 0.015, 0.975)
Vector: 32.234, 259.366, -6.031)

#1: Protein	FIMBRIAE / LONG POLAR FIMBRIAE ADHESIN LPFD Mass: 38626.824 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-350 Source method: isolated from a genetically manipulated source Details: LPFD SELF-COMPLEMENTED BY C-TERMINAL ADDITION OF THE N-TERMINAL EXTENSION OF THE MINOR PILUS SUBUNIT LPFE ATTDLGAKGTLKFSLKISQG Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: LF82 / Description: PROVIDED BY A. DARFEUILLE-MICHAUD / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: E2QGQ5, UniProt: A0A0M3KL51*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	REMOVED FIRST 24 RESIDUES CORRESPONDING TO SIGNAL PEPTIDE, ADDED RESIDUES ...REMOVED FIRST 24 RESIDUES CORRESPONDING TO SIGNAL PEPTIDE, ADDED RESIDUES GGGGGGGGGGATTDLGAKGTLKFSLKISQGHHHHHH AT C- TERMINUS FOR SELF-COMPLEMENTATION

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 % Description: PHASES OBTAINED BY SAD EXPERIMENT ON TYROSINE- IODINATED CRYSTAL
Crystal grow	pH: 8 Details: 0.1 M TRIS PH 8.0, 0.18 M SODIUM CITRATE, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.82→49 Å / Num. obs: 82152 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / B_iso Wilson estimate: 21.2 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 23.95
Reflection shell	Resolution: 1.82→1.87 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 2.63 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.82→48.59 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.251 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	4108	5 %	RANDOM
R_work	0.16701	-	-	-
obs	0.16847	78044	99.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.964 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0 Å²
2-	-	0.2 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→48.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5204	0	12	658	5874

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	5489
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5104
X-RAY DIFFRACTION	r_angle_refined_deg	1.93	1.957	7515
X-RAY DIFFRACTION	r_angle_other_deg	0.854	3.002	11815
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.682	5	720
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.622	25.822	225
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.647	15	870
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.949	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	859
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	6387
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1201
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.818→1.865 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	294	-
R_work	0.266	5594	-
obs	-	-	98.46 %

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	0.9355	0.026	0.2487	1.7373	0.2483	0.5513	0.0038	0.1351	0.0956	-0.0911	-0.0283	-0.0373	0.0017	0.0235	0.0244	0.0817	0.0036	-0.0011	0.0208	0.0068	0.1234	35.352	130.254	61.934
2	1.5373	-0.5151	0.7193	6.0076	-1.5028	1.4914	-0.046	0.0739	0.3781	0.233	-0.1177	-0.1824	-0.257	0.0327	0.1636	0.1145	-0.0049	-0.0209	0.0058	0.02	0.2632	35.258	148.304	68.317
3	0.96	-0.2982	-0.1052	3.7725	0.7254	1.0329	-0.0202	0.1349	0.1658	-0.1187	-0.0177	-0.0149	-0.0309	0.0555	0.0379	0.0903	-0.0124	-0.0332	0.0257	0.0413	0.1744	32.657	138.19	59.437
4	2.8984	-3.9966	0.3235	11.695	-1.4888	0.6148	0.057	0.2199	-0.0016	-0.4721	-0.0268	0.1819	0.0288	0.035	-0.0301	0.1165	-0.0197	-0.0403	0.0386	0.0232	0.1689	39.032	137.761	59.378
5	0.3547	0.4882	0.2594	3.3029	0.9022	0.3939	-0.0387	0.1094	0.0081	0.0119	0.0731	0.0482	0.0537	0.0351	-0.0343	0.115	-0.024	0.0032	0.0506	0.0067	0.155	33.688	112.31	58.018
6	13.9546	9.2324	-0.888	6.3501	0.4135	5.0591	0.1682	0.0879	-0.9292	0.4188	-0.011	-0.5707	1.7766	-0.1754	-0.1572	0.8649	0.0444	-0.0147	0.0762	-0.0441	0.5272	27.877	59.086	59.576
7	4.1684	-5.0624	5.2674	13.5229	-13.1268	15.7816	0.0769	-0.0455	-0.6244	-0.851	-0.2072	0.0563	1.4981	0.4463	0.1303	0.4585	0.0615	0.0942	0.1261	-0.0136	0.2811	33.578	65.901	55.794
8	1.0834	1.1835	-0.7482	4.5216	-1.2364	1.0913	-0.0697	-0.2294	-0.1213	0.1622	-0.0772	-0.2422	0.1119	0.0954	0.147	0.1891	0.0311	0.0066	0.0971	-0.0226	0.1448	36.995	84.274	60.305
9	1.3848	3.0283	-1.1819	11.9595	-2.7946	1.9401	-0.2018	-0.0466	-0.0737	0.0566	0.1819	0.019	0.1896	-0.0703	0.0199	0.1446	0.032	0.0069	0.0863	-0.0224	0.1339	34.95	81.399	56.431
10	2.8864	4.3495	-0.1606	10.7652	0.1254	1.4119	0.0137	-0.2843	-0.102	0.2466	-0.1278	0.1645	0.1128	-0.0113	0.114	0.2103	0.0167	0.0442	0.1093	-0.0033	0.1644	28.411	81.576	62.798
11	0.912	-0.2001	-0.2706	3.0218	-0.0355	0.6465	-0.0576	0.1397	0.0982	-0.0694	0.0781	0.2969	-0.0009	-0.0488	-0.0204	0.0716	-0.0135	-0.0584	0.0259	0.0304	0.1608	11.71	130.198	64.217
12	1.2032	0.5297	-0.1753	9.883	1.6455	1.616	0.0041	0.0616	-0.1384	0.2072	-0.1148	0.0259	0.1913	-0.0757	0.1106	0.0862	-0.0006	-0.0078	0.0089	0.0007	0.1514	12.906	113.281	70.438
13	1.3404	-0.9598	0.1495	3.8946	-0.3393	0.705	0.0004	0.1656	0.0131	-0.2763	-0.0221	0.2621	0.0282	-0.0136	0.0218	0.1211	-0.0236	-0.0398	0.028	-0.0012	0.1332	14.492	121.267	58.663
14	0.8689	-0.6998	0.0472	5.4049	-0.4092	0.6131	-0.0569	0.0465	0.0193	0.1576	0.029	0.1709	0.0105	-0.0281	0.0278	0.0713	-0.0155	-0.0319	0.0077	0.0018	0.1398	12.601	123.778	65.992
15	1.4959	-2.0999	-0.1369	10.2336	1.2747	0.326	-0.0457	0.1721	0.0931	-0.2244	0.0444	0.1921	-0.0052	-0.0308	0.0014	0.1369	-0.0324	-0.0531	0.0665	0.0251	0.1768	8.594	118.879	60.996
16	0.0937	0.0898	0.0089	6.378	-1.0851	0.6084	-0.0476	0.0839	0.1085	-0.1232	-0.0314	-0.3757	-0.1813	0.0176	0.0791	0.1759	-0.0269	-0.0795	0.0788	0.1042	0.3982	13.386	156.973	59.678
17	17.1496	-6.742	6.3685	9.7279	12.0935	33.2294	-0.247	0.4137	1.4214	-0.2668	0.0167	-0.4618	-1.472	0.5317	0.2302	0.9756	-0.1218	0.0361	0.0827	0.1225	0.7351	15.875	201.633	60.308
18	1.5646	1.5544	0.8502	14.7225	-1.1851	4.8988	0.2371	-0.1129	0.1427	0.1859	-0.3834	0.2407	-0.7861	-0.0468	0.1463	0.3903	-0.0152	0.0034	0.0631	0.1126	0.4216	12.079	189.605	54.845
19	1.3435	0.0978	0.0529	7.9951	-1.0241	1.4497	0.1295	-0.1899	0.0606	0.8899	-0.1571	0.1928	-0.5582	0.007	0.0275	0.4608	-0.0263	-0.0151	0.086	0.0893	0.3634	9.835	177.428	64.002
20	1.509	1.3482	0.2031	9.1071	-1.6481	1.2343	0.1454	-0.0489	0.0124	0.5929	-0.27	-0.4061	-0.4016	0.1789	0.1245	0.3594	-0.0399	-0.0707	0.0935	0.1106	0.3976	14.619	177.259	59.877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 40
2	X-RAY DIFFRACTION	2	A	41 - 58
3	X-RAY DIFFRACTION	3	A	59 - 144
4	X-RAY DIFFRACTION	4	A	145 - 161
5	X-RAY DIFFRACTION	5	A	162 - 198
6	X-RAY DIFFRACTION	6	A	199 - 206
7	X-RAY DIFFRACTION	7	A	207 - 219
8	X-RAY DIFFRACTION	8	A	220 - 288
9	X-RAY DIFFRACTION	9	A	289 - 309
10	X-RAY DIFFRACTION	10	A	310 - 353
11	X-RAY DIFFRACTION	11	B	1 - 40
12	X-RAY DIFFRACTION	12	B	41 - 57
13	X-RAY DIFFRACTION	13	B	58 - 112
14	X-RAY DIFFRACTION	14	B	113 - 145
15	X-RAY DIFFRACTION	15	B	146 - 164
16	X-RAY DIFFRACTION	16	B	165 - 201
17	X-RAY DIFFRACTION	17	B	202 - 207
18	X-RAY DIFFRACTION	18	B	208 - 222
19	X-RAY DIFFRACTION	19	B	223 - 284
20	X-RAY DIFFRACTION	20	B	285 - 354

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