PDB-4ipu: Crystal structure of Pseudomonas aeruginosa (strain: PAO1) type I...

ID or keywords:

Entry

Database: PDB / ID: 4ipu

Title

Crystal structure of Pseudomonas aeruginosa (strain: PAO1) type IV minor pilin FimU in space group P21

Components

FimU protein

Keywords

CELL ADHESION / minor pilin / membrane associated

Function / homology

Function and homology information

type IV pilus assembly / type IV pilus / type IV pilus-dependent motility / pilus assembly / protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.351 Å

Authors

Nguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Junop, M.S. / Burrows, L.L.

Citation

Journal: To be Published
Title: Role of minor pilins in Pseudomonas aeruginosa type IV pilus dynamics
Authors: Nguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Harvey, H. / Giltner, C.L. / Junop, M.S. / Burrows, L.L.

History

Deposition	Jan 10, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ipu.cif.gz	221.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ipu.ent.gz	179.3 KB	Display	PDB format
PDBx/mmJSON format	4ipu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ipu_validation.pdf.gz	450.4 KB	Display	wwPDB validaton report
Full document	4ipu_full_validation.pdf.gz	455.6 KB	Display
Data in XML	4ipu_validation.xml.gz	35.2 KB	Display
Data in CIF	4ipu_validation.cif.gz	50.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ip/4ipu ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4ipu	HTTPS FTP

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Related structure data

Related structure data	4ipv
Similar structure data	3aqa-1 6ohh-2 4qqh-d 3mzt-1 3mzt-2 5vbr-2 1qd0-d 3mzt-5 3t3j-d 3zpv-5 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

4ipv

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: FimU protein

B: FimU protein

C: FimU protein

D: FimU protein

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

1

A: FimU protein

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

2

B: FimU protein

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

3

C: FimU protein

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

4

D: FimU protein

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

Unit cell

Length a, b, c (Å)	61.982, 37.246, 103.123
Angle α, β, γ (deg.)	90.00, 105.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	FimU protein Mass: 14737.440 Da / Num. of mol.: 4 / Fragment: unp residues 37-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: fimU / Plasmid: pET151-D-Topo / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: Q59652, UniProt: G3XCZ0*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 821 / 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: 1.95 Å³/Da / Density % sol: 36.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.2 M ammonium formate, 20% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2012 / Details: Mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.35→50 Å / Num. all: 99928 / Num. obs: 99928 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / B_iso Wilson estimate: 14.2 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 20.5
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.424 / Mean I/σ(I) obs: 3.17 / Num. unique all: 4843 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHENIX	(phenix.autosol)	model building
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.351→49.726 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 20.35 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2027	1983	2 %	Random
R_work	0.1763	-	-	-
all	0.1768	99928	-	-
obs	0.1768	99216	98.95 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.351→49.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3886	0	0	821	4707

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4009
X-RAY DIFFRACTION	f_angle_d	1.052	5448
X-RAY DIFFRACTION	f_dihedral_angle_d	12.503	1466
X-RAY DIFFRACTION	f_chiral_restr	0.063	639
X-RAY DIFFRACTION	f_plane_restr	0.004	716

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 (%)
1.3507-1.3844	0.2522	143	0.2472	6439	X-RAY DIFFRACTION	92
1.3844-1.4219	0.2422	134	0.2311	6799	X-RAY DIFFRACTION	98
1.4219-1.4637	0.2553	147	0.2094	6830	X-RAY DIFFRACTION	98
1.4637-1.511	0.2326	129	0.2	6913	X-RAY DIFFRACTION	99
1.511-1.565	0.2046	150	0.1973	6920	X-RAY DIFFRACTION	99
1.565-1.6276	0.1987	147	0.1788	6932	X-RAY DIFFRACTION	100
1.6276-1.7017	0.2123	132	0.1831	6987	X-RAY DIFFRACTION	100
1.7017-1.7914	0.2217	143	0.1839	6967	X-RAY DIFFRACTION	100
1.7914-1.9037	0.2496	138	0.1832	6999	X-RAY DIFFRACTION	100
1.9037-2.0507	0.1859	141	0.175	7009	X-RAY DIFFRACTION	100
2.0507-2.257	0.2038	148	0.163	7009	X-RAY DIFFRACTION	100
2.257-2.5836	0.1917	136	0.1763	7071	X-RAY DIFFRACTION	100
2.5836-3.255	0.1675	144	0.1736	7092	X-RAY DIFFRACTION	100
3.255-49.7594	0.2056	151	0.1608	7266	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	7.9446	0.7111	5.7292	0.8252	0.3492	4.3773	-0.1714	0.0645	0.2874	0.088	0.0123	-0.0241	-0.1876	0.0448	0.1682	0.2249	0.0151	0.0139	0.1734	-0.0186	0.1694	56.1078	16.4997	-14.744
2	5.3712	0.1804	0.1217	2.4669	0.1628	1.7197	-0.0117	0.1977	0.2175	-0.0678	-0.0269	-0.1187	-0.1693	0.1059	0.0566	0.1864	-0.0148	-0.0101	0.1318	0.0211	0.1394	53.422	20.3514	-28.2689
3	5.5518	-1.2275	-1.9384	7.1626	4.07	2.6989	0.0964	0.3847	0.143	-0.5023	-0.0916	-0.138	-0.5945	-0.188	-0.0463	0.2445	0.0524	-0.0014	0.1871	0.0186	0.1631	46.4501	24.6751	-34.5055
4	3.9854	-1.6649	0.3144	2.2079	0.2934	2.6295	-0.0971	0.0028	0.2344	0.0549	0.0362	-0.2348	-0.1626	0.1913	0.046	0.1547	-0.0298	-0.0005	0.102	0.025	0.1197	58.1652	17.6657	-25.3864
5	7.0615	0.4707	1.5121	0.9469	0.2173	1.1154	-0.1056	-0.1233	-0.0301	-0.0344	0.0183	0.0579	-0.0028	-0.0507	0.0743	0.1603	-0.0083	0.0052	0.131	-0.0067	0.1422	50.5473	8.402	-26.899
6	7.3747	4.4313	-3.0696	2.7795	-2.1092	2.0909	0.3255	-0.1328	-0.0686	0.1962	-0.1484	-0.8665	-0.1029	1.378	-0.222	0.2396	-0.0258	-0.0333	0.4334	0.008	0.2945	71.5249	10.7107	-18.5326
7	3.4959	-0.6736	1.2483	1.0345	0.0054	2.6399	0.0913	-0.1831	-0.2072	0.1027	-0.0201	0.0103	0.2125	-0.0857	-0.0764	0.1824	-0.0004	-0.0023	0.1192	0.009	0.1432	56.8587	6.0511	-18.8644
8	4.218	1.0481	3.6349	8.9477	3.5341	3.9512	0.3347	-0.0544	0.6015	0.4726	0.2836	-0.3117	-1.259	0.1103	-0.5834	0.7545	-0.1166	0.1941	0.4014	-0.0672	0.5686	35.6543	30.8131	33.602
9	2.5316	-2.3636	1.0273	3.4156	-2.0609	2.8799	0.0913	0.1208	0.1357	-0.1692	-0.1752	-0.1973	-0.051	0.1455	0.0793	0.1494	0.0023	0.0017	0.1861	-0.0008	0.166	37.9048	12.9516	46.09
10	3.8026	-1.7621	1.3234	2.7658	-1.3398	2.9899	-0.0374	-0.1874	0.1557	0.1437	-0.0408	0.0353	-0.2431	-0.0431	0.0804	0.1453	-0.01	0.0048	0.1835	-0.0158	0.1322	37.5594	18.5175	56.8815
11	1.8084	-0.4908	-0.1319	2.2775	-0.8091	1.7852	-0.0342	0.0219	0.2171	0.0359	0.0535	-0.0137	-0.2339	-0.1559	-0.0064	0.1673	0.0292	-0.0128	0.1728	-0.0223	0.1415	32.5247	21.7789	50.903
12	1.6708	-0.7031	0.6551	2.933	-0.9641	1.1208	0.0703	0.1514	-0.2056	-0.1181	0.0287	0.0882	0.1101	-0.0226	-0.1021	0.1237	0.012	-0.007	0.1919	-0.007	0.1469	28.2162	9.5825	49.9672
13	3.7487	-2.3147	-0.8441	3.2315	1.9017	2.1897	-0.3535	-0.2633	0.3994	-0.5064	0.796	0.1035	-0.4061	-0.2038	-0.3842	0.2487	-0.0503	-0.057	0.3346	0.0541	0.1961	22.4397	23.8441	42.8519
14	1.9747	-0.9655	-1.5751	4.9416	2.5711	4.4197	-0.2692	-0.27	-0.182	-0.273	0.4822	0.4075	0.026	0.0737	-0.2447	0.1551	-0.0213	-0.0459	0.2877	0.0606	0.2045	23.4098	14.7374	41.8779
15	8.4773	-0.1663	6.1044	0.4623	-0.3073	4.875	-0.0803	0.1226	0.0487	0.0131	0.0558	-0.0176	-0.2266	-0.0464	0.0202	0.1789	0.014	0.0251	0.1672	-0.0103	0.1826	42.1236	16.4746	35.1943
16	7.5097	0.0231	1.7863	4.2979	-0.9079	3.427	0.0289	0.806	0.078	-0.1594	-0.1451	-0.2741	-0.101	0.2618	0.1019	0.1847	0.0152	0.0325	0.2307	0.0063	0.1365	38.9771	19.1096	21.9504
17	0.9045	0.5998	-0.7023	0.8333	0.3703	8.1159	0.1914	0.7801	0.127	-1.0013	-0.0371	-0.4321	-1.0126	0.1284	-0.202	0.3754	0.0633	0.0815	0.3785	0.0211	0.1811	34.6916	24.6615	15.5517
18	4.1637	-3.2942	1.257	5.9538	0.0382	2.8643	-0.3489	0.3491	0.4614	0.2913	0.3079	-1.1092	-0.1463	0.3193	0.1504	0.1611	-0.0394	-0.0015	0.158	0.0131	0.2394	47.7302	20.4532	29.4566
19	4.0541	-0.6562	-0.9813	4.2466	-0.3391	3.9959	-0.0288	0.3769	-0.3945	-0.2679	0.196	0.3286	0.3506	-0.1075	-0.1438	0.1952	0.01	-0.025	0.2326	-0.0622	0.2339	33.7554	9.8189	20.6001
20	3.787	0.265	0.6504	2.7742	0.424	3.5674	0.2187	-0.365	-0.4622	-0.0465	-0.0411	-0.2314	0.1727	-0.0295	-0.1093	0.1829	0.0152	0.0133	0.1911	-0.0172	0.2743	48.7718	8.1679	31.2778
21	4.6762	4.0885	6.1844	5.1455	4.9645	8.5755	0.2035	-0.5999	-0.3629	0.3556	-0.3943	0.4017	0.5807	-0.7199	0.3448	0.2297	-0.044	-0.0072	0.2992	-0.0043	0.3784	32.806	5.6556	30.0622
22	6.5861	-0.4205	-5.0967	2.3121	-0.5925	9.3227	-0.151	-0.1486	-0.6701	-0.0268	0.0812	-0.1105	0.5837	0.0368	0.1927	0.2461	0.009	-0.0057	0.2202	0.0097	0.3439	47.5577	3.1564	34.2097
23	4.7133	-3.9426	2.1251	3.3423	-2.2746	3.7748	-0.0221	0.0816	0.3718	0.146	-0.163	-0.3629	-0.4052	-0.073	0.1288	0.2426	0.0156	0.0127	0.196	-0.0067	0.1965	50.8311	16.3317	-7.1452
24	2.134	-1.2433	-0.2756	5.0175	0.471	0.9646	-0.0633	-0.1282	0.1145	0.6065	0.0312	0.1068	-0.0578	-0.0042	0.0007	0.2459	-0.0033	0.0225	0.1222	-0.0096	0.1342	51.4459	17.0379	4.2996
25	1.9125	-0.146	0.2534	3.6133	0.4186	1.2502	-0.0111	-0.1668	0.0575	0.3712	0.0567	-0.0747	0.1662	-0.0056	-0.0773	0.2808	0.0039	-0.0187	0.1417	-0.0114	0.1555	55.9238	20.3341	3.1637
26	2.485	-1.9233	0.1422	7.3051	0.9055	0.9463	0.0508	-0.2373	-0.0798	0.3514	-0.0145	0.3989	0.0448	-0.1359	-0.0194	0.2354	-0.0007	0.0838	0.1727	0.0006	0.2072	44.3658	11.7023	2.8872
27	4.8661	0.3542	-1.0285	7.6707	-2.2777	3.4186	0.0197	-0.0599	0.0385	0.1814	0.0371	0.6604	-0.223	-0.2126	-0.0531	0.2156	0.0234	0.0436	0.2205	-0.0243	0.3233	39.5718	19.1153	-1.899
28	5.9384	-1.5034	3.1242	5.1452	-1.0991	5.8595	0.3781	-0.2128	0.2797	-0.6296	-0.0381	0.7782	-0.5809	-0.4628	-0.2921	0.452	0.1703	-0.0262	0.4235	-0.0648	0.6832	34.7438	30.1806	-5.5269
29	4.8527	-1.3951	-0.8158	4.5238	0.6598	4.0595	0.2177	0.2632	-0.1487	-0.9575	-0.3189	1.0751	-0.0392	-0.416	0.0061	0.2943	0.0388	-0.0983	0.2225	-0.0201	0.3767	38.444	16.041	-7.7469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 75 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 76 through 86 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 87 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 128 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 129 through 135 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 136 through 159 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 31 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 32 through 62 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 63 through 86 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 87 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 128 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 129 through 140 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 141 through 159 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 24 through 54 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 55 through 75 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 76 through 86 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 87 through 101 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 102 through 121 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 122 through 140 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 141 through 148 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 149 through 159 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 31 through 54 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 55 through 75 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 76 through 96 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 97 through 121 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 122 through 128 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 129 through 135 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 136 through 159 )

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Yorodumi