PDB-6ok2: PilT4 from Geobacter metallireducens bound to ADP: C3ocococ confo...

ID or keywords:

Entry

Database: PDB / ID: 6ok2

Title

PilT4 from Geobacter metallireducens bound to ADP: C3ocococ conformation

Components

Twitching motility pilus retraction ATPase

Keywords

MOTOR PROTEIN / T4P / ATPase / type IV pilus / motor

Function / homology

Function and homology information

ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function

Biological species

Geobacter metallireducens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.287 Å

Authors

McCallum, M. / Howell, P.L.

Funding support

Canada, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: Multiple conformations facilitate PilT function in the type IV pilus.
Authors: Matthew McCallum / Samir Benlekbir / Sheryl Nguyen / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell /

Abstract: Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by ...

History

Deposition	Apr 12, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 27, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ok2.cif.gz	814 KB	Display	PDBx/mmCIF format
PDB format	pdb6ok2.ent.gz	682.7 KB	Display	PDB format
PDBx/mmJSON format	6ok2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ok2_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	6ok2_full_validation.pdf.gz	1.9 MB	Display
Data in XML	6ok2_validation.xml.gz	72.3 KB	Display
Data in CIF	6ok2_validation.cif.gz	95.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/6ok2 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/6ok2	HTTPS FTP

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Related structure data

Related structure data	20114C 20115C 20116C 20117C 6ojxC 6ojyC 6ojzC 6okvC 6oljC 6olkC 6ollC 6olmC 3jvvS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ojy-d 6ojz-d 6olk-d 3jvu-1 3jvv-1 6okv-d 6fo1-d 6geb-2 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
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: Twitching motility pilus retraction ATPase

B: Twitching motility pilus retraction ATPase

C: Twitching motility pilus retraction ATPase

D: Twitching motility pilus retraction ATPase

E: Twitching motility pilus retraction ATPase

F: Twitching motility pilus retraction ATPase

hetero molecules

260 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: microscopy, CryoEM evidence for hexamer

Unit cell

Length a, b, c (Å)	111.817, 120.956, 185.915
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Twitching motility pilus retraction ATPase Mass: 42883.379 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210) (bacteria) Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: pilT-4, Gmet_1394 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q39VU6
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 5.75 % (w/v) PEG3350 100 mM L-proline 50 mM Hepes pH 7.6 100 mM NaCl 25 mM Hepes pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9996 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9996 Å / Relative weight: 1
Reflection	Resolution: 3.287→29.386 Å / Num. obs: 38771 / % possible obs: 99 % / Redundancy: 6.7 % / R_pim(I) all: 0.069 / Net I/σ(I): 7.5
Reflection shell	Resolution: 3.287→3.4 Å / Num. unique obs: 3597 / R_pim(I) all: 0.501

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3JVV

3jvv

Resolution: 3.287→29.386 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7

	R_factor	Num. reflection	% reflection
R_free	0.2555	3654	4.99 %
R_work	0.2154	-	-
obs	0.2174	38771	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.287→29.386 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16026	0	162	12	16200

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	16486
X-RAY DIFFRACTION	f_angle_d	0.577	22463
X-RAY DIFFRACTION	f_dihedral_angle_d	14.95	10023
X-RAY DIFFRACTION	f_chiral_restr	0.041	2679
X-RAY DIFFRACTION	f_plane_restr	0.004	2913

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 (%)
3.287-3.3302	0.39	110	0.3971	2224	X-RAY DIFFRACTION	83
3.3302-3.3758	0.3645	142	0.344	2714	X-RAY DIFFRACTION	100
3.3758-3.4239	0.3888	147	0.3396	2709	X-RAY DIFFRACTION	100
3.4239-3.4749	0.3165	145	0.3178	2696	X-RAY DIFFRACTION	100
3.4749-3.5292	0.36	136	0.3146	2692	X-RAY DIFFRACTION	100
3.5292-3.5869	0.3277	148	0.3039	2725	X-RAY DIFFRACTION	100
3.5869-3.6487	0.3193	141	0.2923	2703	X-RAY DIFFRACTION	100
3.6487-3.7149	0.2844	147	0.2864	2683	X-RAY DIFFRACTION	100
3.7149-3.7862	0.2859	141	0.2747	2716	X-RAY DIFFRACTION	100
3.7862-3.8633	0.3183	131	0.2677	2704	X-RAY DIFFRACTION	100
3.8633-3.9471	0.2911	145	0.2574	2719	X-RAY DIFFRACTION	100
3.9471-4.0387	0.2994	155	0.2458	2702	X-RAY DIFFRACTION	100
4.0387-4.1394	0.2365	133	0.2301	2689	X-RAY DIFFRACTION	100
4.1394-4.251	0.2556	144	0.2173	2666	X-RAY DIFFRACTION	100
4.251-4.3757	0.2633	130	0.2167	2695	X-RAY DIFFRACTION	100
4.3757-4.5165	0.2488	152	0.2008	2732	X-RAY DIFFRACTION	100
4.5165-4.6773	0.2355	145	0.1963	2680	X-RAY DIFFRACTION	99
4.6773-4.8638	0.2682	133	0.192	2658	X-RAY DIFFRACTION	98
4.8638-5.0841	0.2265	140	0.194	2673	X-RAY DIFFRACTION	99
5.0841-5.3506	0.2944	137	0.2103	2672	X-RAY DIFFRACTION	99
5.3506-5.6836	0.2726	141	0.2202	2671	X-RAY DIFFRACTION	99
5.6836-6.1187	0.2652	146	0.2313	2683	X-RAY DIFFRACTION	99
6.1187-6.7278	0.281	144	0.2297	2694	X-RAY DIFFRACTION	99
6.7278-7.6861	0.2738	139	0.2029	2688	X-RAY DIFFRACTION	99
7.6861-9.6268	0.1636	145	0.1404	2677	X-RAY DIFFRACTION	99
9.6268-29.387	0.1811	137	0.1383	2698	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	2.7614	-0.1666	-0.5209	2.8146	1.108	3.8465	-0.0729	-0.0453	-0.0194	0.1687	0.0325	-0.2109	0.1785	0.0846	0.0065	0.903	-0.1031	-0.0578	0.6656	-0.0525	0.7664	4.8926	-7.0466	-9.9174
2	4.1689	1.2695	-0.1622	3.7609	-0.37	6.2091	0.1213	-0.5249	-0.0014	0.3956	-0.2839	-0.0471	0.5127	-0.4518	0.1573	0.7287	-0.02	-0.0525	0.6255	-0.0886	0.6195	27.9347	-22.5181	-15.4123
3	4.7847	1.3699	-3.8126	4.2073	-0.8303	4.6381	-0.5335	0.2521	-0.8381	0.009	0.1272	-0.0595	1.1116	-0.299	0.4296	0.8629	0.0114	-0.0072	0.5446	-0.0552	0.7523	19.4282	-39.901	-16.909
4	4.5358	0.1341	-2.0593	3.3818	-0.0762	3.2164	0.3679	0.2842	-0.39	-0.3959	-0.5199	-0.225	-0.7041	0.5362	0.1659	0.8899	-0.2281	-0.1178	0.9975	0.0027	0.9882	46.624	-7.4597	-21.3071
5	4.7861	0.7582	-1.8533	5.7424	0.7548	3.8362	0.1695	0.2569	0.1978	-0.4601	0.0696	-0.153	-0.9612	0.5996	-0.204	1.0394	-0.0783	-0.1055	0.7243	-0.0883	0.6673	39.5508	-7.3714	-26.2088
6	1.9572	2.5377	0.6049	4.3979	-0.7361	5.3455	0.3158	0.0836	-0.395	0.7662	-0.1523	-0.6697	0.1106	0.6846	-0.1207	0.775	0.1411	-0.0191	1.0056	0.0275	0.7932	48.2127	-20.3222	-47.3083
7	4.6864	-0.1925	0.1471	5.3594	-1.9327	3.3869	-0.2546	0.6562	0.108	-0.7365	0.3252	0.8235	-0.0184	-0.9619	-0.1053	0.8239	0.0649	-0.1131	1.0389	-0.0168	0.7815	35.9088	-20.317	-53.3771
8	6.2736	0.6924	-1.4861	5.3665	0.4985	2.4455	-0.6687	-0.1403	-0.4738	-0.1514	-0.4757	0.8633	0.9726	-0.7991	1.1957	1.2413	0.0086	0.1918	0.9479	-0.2797	0.9019	31.9477	-32.4945	-50.1176
9	5.963	-3.4779	0.5449	4.6566	-2.647	4.461	-0.6857	-0.6897	-1.8369	0.5097	0.4113	0.6615	0.9837	-0.0953	0.3177	1.12	0.2234	0.3181	0.965	0.0736	1.4234	42.3943	-42.6064	-40.9287
10	3.4877	-1.3378	-0.7213	4.4261	-0.25	3.2066	0.0299	0.5803	0.9758	-0.561	0.1688	-0.5679	-0.8643	0.3188	-0.1216	1.1129	-0.1289	0.1268	0.9116	0.0392	0.8877	46.6823	-2.0737	-63.1216
11	3.7441	-1.5183	2.009	3.5616	-0.4135	4.4758	0.0944	0.0182	-0.0558	0.2212	-0.0522	0.0596	0.3657	0.1006	-0.011	0.5921	-0.0076	0.0719	0.6336	-0.0612	0.5326	31.3549	-23.2662	-79.2889
12	5.5948	0.6261	-0.0459	2.8187	-0.8559	4.1203	0.2906	0.035	-1.1446	-0.4936	-0.3	-0.0527	1.2407	0.4066	0.066	1.0981	0.1577	-0.0474	0.8366	0.0202	0.9649	38.8532	-41.8171	-79.5785
13	5.6606	-1.1881	1.6472	4.0929	0.4688	3.1243	0.7817	0.3744	-1.446	-0.366	-0.0112	-1.0447	0.6808	1.1006	-0.7083	0.8678	0.1933	-0.0841	1.5064	-0.1871	1.2527	54.712	-38.4335	-73.1187
14	2.8745	-0.195	1.4903	6.2507	1.1049	5.3686	0.095	0.0543	0.189	0.0888	-0.1146	0.5262	-0.0263	-0.4965	0.0254	0.5765	-0.0743	0.0712	0.6882	0.0176	0.6632	14.4316	-5.0405	-90.5783
15	2.6627	-1.1221	-0.7237	7.5224	-0.1394	2.821	-0.1979	-0.3215	-0.0403	0.2732	0.1992	-0.3953	-0.1188	0.4498	0.0043	0.4106	-0.0793	-0.0188	0.5975	-0.0335	0.5758	-2.8756	-29.7553	-75.2686
16	4.8399	-0.7735	-0.7957	5.4937	0.7244	6.3066	-0.3948	0.0933	-0.5553	-0.5317	0.0382	-0.4681	0.8746	0.452	0.3107	0.9355	0.0016	0.1366	0.8286	-0.0059	0.8772	8.0948	-48.7244	-85.9143
17	4.8593	-0.1443	-0.8973	6.4066	1.373	6.6876	-0.2094	0.0001	0.4878	-0.08	-0.0636	0.4224	-1.3956	-0.6425	0.2812	0.7643	0.0995	-0.0818	0.5921	0.0198	0.634	-18.3687	-5.2947	-75.2362
18	4.4973	-0.7061	-1.2071	3.0103	0.7993	7.3565	0.0267	-0.1029	-0.2072	-0.1092	-0.4747	0.9151	-0.4666	-1.9012	0.4991	0.592	-0.0837	0.0347	1.1839	-0.2269	0.8827	-33.5965	-24.5881	-57.4417
19	5.4055	0.0782	1.4172	5.6861	0.1375	2.9425	0.0354	0.3625	-0.0402	-0.2488	-0.3283	0.3574	0.1109	-0.778	0.3145	0.7055	-0.0399	-0.0573	0.8431	-0.123	0.6063	-22.8934	-17.1497	-48.6047
20	2.3505	-0.9074	0.8431	3.9912	-0.3236	5.3523	-0.0315	-0.1026	-0.5267	0.3	0.1631	0.1051	1.1008	-0.2197	-0.0792	0.8577	-0.2392	0.0139	0.6965	-0.0778	0.7259	-23.4224	-37.1266	-55.3033
21	3.1096	0.3295	1.4711	6.1149	0.9488	4.8758	0.3494	0.1776	-0.4374	-0.2778	0.0748	0.5693	1.4767	-0.4703	-0.3137	1.126	-0.2146	-0.0631	1.1415	-0.1627	0.8864	-33.6387	-40.7834	-72.6767
22	5.7612	-0.1874	-0.3168	4.8666	2.2606	5.3786	-0.438	-0.9484	0.5945	0.6828	-0.2772	1.2306	-0.483	-2.1124	0.859	0.911	0.2545	-0.0305	1.3472	-0.344	0.8872	-33.1468	-8.0068	-34.0679
23	5.3673	0.2752	0.7744	2.8406	0.0392	5.8589	-0.8366	-0.5083	0.8844	0.065	-0.1082	0.0165	-0.493	-0.4362	0.7977	1.061	0.0742	-0.1373	0.6896	-0.1568	0.8756	-18.9291	-6.1833	-35.2515
24	4.9666	-0.5702	-0.4545	2.8682	0.7042	4.1321	-0.0938	-0.3006	-0.4009	0.6186	-0.1386	-0.0401	0.2252	-0.4873	0.2166	1.1762	-0.1361	-0.0991	0.8915	-0.0098	0.8727	-13.3611	-29.3422	-18.9954
25	4.0817	-1.0522	-0.285	6.6073	0.8719	5.0241	-0.1587	0.346	0.0407	-0.0368	0.0751	0.0003	0.3095	-0.2383	0.128	0.6208	-0.0948	0.0156	0.5797	-0.0387	0.5791	-2.7034	-20.2934	-23.3568
26	3.2897	-2.6363	-0.8866	3.7811	-1.0132	2.4748	0.0063	0.5899	-0.7694	-0.1544	-0.3094	-0.2532	0.6189	-0.0287	0.3552	1.012	-0.1749	-0.0852	0.7578	-0.1151	1.082	-4.9051	-38.8779	-31.5079
27	4.9473	0.2978	-0.4579	2.9266	-0.0158	1.5168	0.1759	-0.1687	-1.3311	-0.2418	-0.3146	-0.0123	0.6121	-0.5902	-0.0493	1.4302	-0.299	-0.0158	1.0396	-0.0543	1.2737	-21.7728	-46.1414	-30.387

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 100 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 101 through 202 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 203 through 353 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 27 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 100 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 101 through 185 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 186 through 233 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 234 through 271 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 272 through 353 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 99 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 100 through 285 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 286 through 328 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 329 through 353 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -4 through 100 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 101 through 309 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 310 through 356 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 100 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 101 through 151 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 152 through 208 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 209 through 309 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 310 through 353 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 2 through 44 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 45 through 100 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 101 through 151 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 152 through 233 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 234 through 310 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 311 through 352 )

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About Yorodumi

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Yorodumi