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

ID or keywords:

Entry

Database: PDB / ID: 4ipv

Title

Crystal structure of Pseudomonas aeruginosa (strain: PAO1) type IV minor pilin FimU in space group P65

Components

FimU protein

Keywords

CELL ADHESION / Minor pilin / Membrane associated

Function / homology

Function and homology information

type IV pilus /

type IV pilus assembly / 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 /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

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

Citation

Journal: To be Published
Title: Minor pilin FimU controls P. aeruginosa type IV pilus extension/retraction dynamics independently of other minor components
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	Sep 20, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ipv.cif.gz	115.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ipv.ent.gz	89.5 KB	Display	PDB format
PDBx/mmJSON format	4ipv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ip/4ipv ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4ipv	HTTPS FTP

-
Related structure data

Related structure data	4ipuS S: Starting model for refinement
Similar structure data	5wbh-5 5yiz-9 5yj0-15 5yiz-10 3oa1-1 4zg1-6 4zg1-1 2vzp-2 1aue-2 5yj0-14 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

-
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

29.4 kDa, 2 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)

Unit cell

Length a, b, c (Å)	40.687, 40.687, 272.922
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	FimU protein Mass: 14690.546 Da / Num. of mol.: 2 / 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 / Water Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

FimU protein

Mass: 14690.546 Da / Num. of mol.: 2 / 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 /

Water

Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.58 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium chloride, 0.1 M Tris-HCl, 25% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / 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: 1.1 Å / Relative weight: 1
Reflection	Resolution: 1.4→50 Å / Num. all: 49829 / Num. obs: 49829 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.4 % / B_iso Wilson estimate: 12.94 Å² / R_merge(I) obs: 0.044 / Net I/σ(I): 53.8
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 8.7 % / R_merge(I) obs: 0.354 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2305 / % possible all: 93.9

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4IPU

4ipu

Resolution: 1.4→35.236 Å / SU ML: 0.1 / σ(F): 0 / Phase error: 19.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1959	1952	3.98 %	Random
R_work	0.1642	-	-	-
all	0.1655	49829	-	-
obs	0.1655	48996	98.02 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→35.236 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1808	0	0	528	2336

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1851
X-RAY DIFFRACTION	f_angle_d	1.022	2514
X-RAY DIFFRACTION	f_dihedral_angle_d	11.279	660
X-RAY DIFFRACTION	f_chiral_restr	0.062	300
X-RAY DIFFRACTION	f_plane_restr	0.003	328

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 (%)
1.3997-1.4347	0.2369	123	0.2027	3010	X-RAY DIFFRACTION	88
1.4347-1.4735	0.2276	129	0.1882	3196	X-RAY DIFFRACTION	93
1.4735-1.5169	0.2096	141	0.1774	3337	X-RAY DIFFRACTION	97
1.5169-1.5658	0.2042	141	0.1683	3384	X-RAY DIFFRACTION	98
1.5658-1.6218	0.1713	141	0.1596	3341	X-RAY DIFFRACTION	99
1.6218-1.6867	0.2049	139	0.1685	3405	X-RAY DIFFRACTION	99
1.6867-1.7635	0.2041	141	0.173	3435	X-RAY DIFFRACTION	100
1.7635-1.8565	0.2206	141	0.1697	3410	X-RAY DIFFRACTION	100
1.8565-1.9728	0.2053	146	0.1583	3374	X-RAY DIFFRACTION	100
1.9728-2.1251	0.1758	140	0.1601	3445	X-RAY DIFFRACTION	100
2.1251-2.3389	0.2043	146	0.157	3412	X-RAY DIFFRACTION	100
2.3389-2.6772	0.2053	145	0.1695	3423	X-RAY DIFFRACTION	100
2.6772-3.3726	0.1864	139	0.1649	3460	X-RAY DIFFRACTION	100
3.3726-35.2471	0.1826	140	0.1565	3412	X-RAY DIFFRACTION	99

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	2.0546	1.8936	-0.2173	5.2817	-0.5016	3.057	-0.0235	0.0139	0.048	-0.2078	0.0021	0.027	-0.0624	0.0248	0.0221	0.1097	0.0188	-0.0168	0.0869	0.0044	0.117	-17.933	13.1642	-11.4831
2	3.6693	3.2702	2.6633	6.6974	3.3855	3.4469	0.1133	0.0182	-0.3591	0.4376	0.112	-0.3068	0.6274	0.0361	-0.2755	0.2293	0.0024	-0.0047	0.0928	0.009	0.1733	-17.3724	1.6684	-4.6743
3	4.7005	1.2271	1.6616	4.6851	5.1967	7.587	0.0098	-0.212	0.2183	0.1784	0.0283	-0.3569	0.0176	0.1449	-0.0337	0.1133	-0.0032	-0.0327	0.0744	0.0255	0.1223	-12.2421	14.528	0.2538
4	5.4251	0.5004	-3.5579	1.9566	-0.2878	8.9437	0.0654	-0.3849	-0.263	0.0538	-0.0892	0.005	0.0739	0.2827	0.0107	0.2108	0.0367	-0.0188	0.1129	0.0308	0.1697	-10.8565	1.2622	0.6284
5	3.2413	0.85	0.5737	3.6212	4.8881	7.3613	-0.0369	-0.0115	0.5241	-0.6171	0.2588	-0.5085	-0.5262	0.3985	-0.2756	0.138	-0.0263	-0.0033	0.1282	0.0266	0.2293	-8.7891	17.4333	-6.465
6	7.048	5.7377	-6.0825	4.7642	-5.446	7.8489	0.0169	-0.2042	0.2149	0.1564	-0.0551	0.0839	-0.2733	0.2418	0.0598	0.1774	0.0139	-0.015	0.1285	0.0008	0.1951	-16.6424	23.1028	-0.1378
7	3.3557	-0.8545	-1.5043	7.5579	5.6963	4.6118	0.0894	-0.0469	-0.1318	0.2492	0.0103	0.067	0.2848	-0.2705	-0.1248	0.173	-0.0009	0.0056	0.1281	0.0235	0.1233	-21.9093	11.1104	2.8214
8	1.7505	-2.1027	-1.9929	4.723	4.1504	6.9587	-0.0745	-0.0143	-0.3584	-0.0318	-0.0536	0.4776	0.427	-0.4048	0.1638	0.2063	-0.0776	0.0131	0.1473	0.0002	0.2444	-27.8671	3.25	-3.5172
9	7.045	6.4699	-1.2805	6.9102	-0.8789	1.2459	-0.014	0.0186	0.3801	0.0079	0.0186	0.3587	-0.1462	-0.119	0.0072	0.1605	0.0266	-0.0095	0.1166	0.0024	0.1429	-23.2014	19.7389	-1.7937
10	7.6601	-3.7694	4.0006	6.3995	1.5918	7.3998	-0.2149	-0.2175	0.4745	0.0656	0.3097	-0.3756	-0.7097	-0.035	-0.1199	0.2664	0.0322	-0.0126	0.1355	-0.0129	0.2547	-20.388	32.3962	-1.3505
11	7.8971	6.6908	-4.978	5.8894	-4.7585	4.5128	-0.0113	0.1252	0.0478	-0.4088	0.0157	0.1311	-0.2011	-0.0904	0.0111	0.1979	0.0383	-0.0387	0.1196	0.0043	0.1642	-25.1718	21.0958	-7.3618
12	6.9844	1.9376	-4.795	6.5006	-2.6137	3.5681	-0.5347	0.1894	-0.6034	-0.3663	0.1664	-0.1244	0.3939	-0.3858	0.3795	0.2175	-0.0301	-0.012	0.1455	-0.012	0.2539	-29.256	10.8646	-8.3673
13	3.4163	-1.3816	3.9053	2.6567	0.6464	8.7074	-0.0408	-0.1437	-0.1601	-0.2017	-0.0475	0.2911	-0.4579	-0.4931	0.0929	0.2177	0.0538	-0.0118	0.147	0.0034	0.2154	-27.6942	26.3796	-5.1717
14	4.2385	-2.0244	0.0902	3.7444	-0.0502	3.9278	-0.1817	-0.0989	0.0608	0.0799	0.0737	0.0699	-0.1873	0.1498	0.0458	0.1658	0.0284	-0.0414	0.0987	-0.0085	0.1067	-21.3227	19.1618	-20.4805
15	4.0289	-2.6389	-1.7948	2.3968	1.4293	0.8952	0.1098	0.1037	0.1402	-0.1707	-0.1806	0.1336	-0.8184	-0.3199	-0.0272	0.3226	0.0856	-0.0713	0.1608	0.001	0.1768	-28.1327	28.2559	-26.094
16	5.9624	-1.9237	-2.4908	2.3618	3.9001	7.6456	-0.085	0.3877	0.0406	-0.4273	0.1044	-0.2426	-0.578	0.3797	0.0293	0.2063	-0.0343	-0.0214	0.1974	0.0537	0.1344	-17.0785	19.9282	-33.2866
17	1.6416	0.2249	1.1918	2.1598	-0.0126	2.5931	-0.0964	0.291	0.2263	-0.1415	-0.0551	-0.1926	-0.4897	0.207	0.1733	0.2371	-0.0337	-0.0289	0.2022	0.0354	0.1553	-17.875	23.3602	-30.1562
18	3.39	-2.5739	0.2305	9.4366	4.1102	5.8169	0.0492	0.258	0.0506	-0.3994	-0.1128	0.2032	-0.2935	-0.0358	0.0771	0.1823	0.0432	-0.0471	0.1337	0.0075	0.1325	-26.8806	17.4464	-34.3856
19	0.8535	-0.6451	-1.1072	4.1435	1.822	3.7443	-0.1258	-0.1664	0.0179	-0.0059	0.0356	0.3778	-0.1495	-0.3921	0.0665	0.1605	0.0525	-0.0476	0.148	-0.0253	0.1734	-30.152	15.753	-27.8433
20	0.6383	-0.0729	-0.0388	0.0458	-0.0704	0.1519	0.0301	0.0962	-0.2159	-0.0782	-0.0463	0.1808	0.0387	0.0156	0.0847	0.4242	0.245	-0.0501	0.3135	-0.059	0.2746	-14.64	0.5845	-30.8471
21	3.6482	-3.7074	4.1318	4.8515	-3.8624	5.1037	-0.059	-0.2954	-0.0753	0.1282	-0.0129	-0.1217	0.3229	0.1382	0.091	0.1897	0.0283	-0.0328	0.1609	-0.0023	0.1695	-22.6679	7.7221	-23.8222
22	3.3599	-3.0924	4.7331	5.4962	-2.7227	7.6745	-0.4999	-0.9362	0.2272	0.3374	0.0496	0.4343	-0.0426	-0.6749	0.3716	0.1908	0.0743	-0.0045	0.2785	-0.0348	0.2763	-31.7161	13.3276	-21.7623
23	1.9479	-0.9461	-2.0745	4.5139	-0.4289	7.1342	-0.1242	-0.0328	-0.5228	0.1909	-0.0925	0.1126	0.7939	0.0371	0.2286	0.3366	0.0463	-0.0456	0.1694	-0.002	0.3	-22.0925	2.0037	-25.6445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 75 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 76 through 86 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 87 through 96 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 97 through 101 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 102 through 110 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 111 through 121 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 122 through 128 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 129 through 135 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 136 through 140 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 141 through 148 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 149 through 159 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 33 through 54 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 55 through 62 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 63 through 75 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 76 through 101 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 102 through 110 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 111 through 128 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 129 through 135 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 136 through 140 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 141 through 148 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 149 through 159 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi