PDB-6ojz: PilT4 from Geobacter metallireducens bound to ADP with partial oc...

ID or keywords:

Entry

Database: PDB / ID: 6ojz

Title

PilT4 from Geobacter metallireducens bound to ADP with partial occupancy: 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: 3.027 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	6ojz.cif.gz	836.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ojz.ent.gz	696.2 KB	Display	PDB format
PDBx/mmJSON format	6ojz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ojz_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	6ojz_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6ojz_validation.xml.gz	73.1 KB	Display
Data in CIF	6ojz_validation.cif.gz	98 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojz ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojz	HTTPS FTP

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Related structure data

Related structure data	20114C 20115C 20116C 20117C 6ojxC 6ojyC 6ok2C 6okvC 6oljC 6olkC 6ollC 6olmC 3jvvS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ok2-d 6ojy-d 6olk-d 6geb-2 6geb-1 6okv-d 3jvv-1 3jvu-1 6fo1-d 6ojx-1 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 of hexamer

Unit cell

Length a, b, c (Å)	112.335, 121.134, 187.112
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 / Comment: ADP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.47 Å³/Da / Density % sol: 50.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 5.75 % (w/v) PEG3350 100 mM L-proline 50 mM Hepes pH 7.1 100 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-2 / Wavelength: 1.2821 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2821 Å / Relative weight: 1
Reflection	Resolution: 3→30 Å / Num. obs: 49747 / % possible obs: 98 % / Redundancy: 12.5 % / R_pim(I) all: 0.047 / Net I/σ(I): 12
Reflection shell	Resolution: 3→3.1 Å / Num. unique obs: 4342 / R_pim(I) all: 0.243

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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: 3.027→29.894 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2321	3800	4.03 %
R_work	0.1945	-	-
obs	0.196	49622	98.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.027→29.894 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16239	0	162	50	16451

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	16836
X-RAY DIFFRACTION	f_angle_d	1.077	22936
X-RAY DIFFRACTION	f_dihedral_angle_d	16.285	10281
X-RAY DIFFRACTION	f_chiral_restr	0.064	2709
X-RAY DIFFRACTION	f_plane_restr	0.008	2975

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 (%)
3.0271-3.0654	0.3782	94	0.3311	1922	X-RAY DIFFRACTION	57
3.0654-3.1057	0.2829	133	0.2846	3453	X-RAY DIFFRACTION	100
3.1057-3.1482	0.3067	144	0.28	3375	X-RAY DIFFRACTION	100
3.1482-3.1931	0.3112	127	0.2721	3481	X-RAY DIFFRACTION	100
3.1931-3.2407	0.2718	133	0.2545	3378	X-RAY DIFFRACTION	100
3.2407-3.2913	0.2683	190	0.249	3385	X-RAY DIFFRACTION	100
3.2913-3.3452	0.2502	108	0.2465	3419	X-RAY DIFFRACTION	100
3.3452-3.4028	0.3268	136	0.2598	3465	X-RAY DIFFRACTION	100
3.4028-3.4646	0.3512	170	0.2798	3355	X-RAY DIFFRACTION	99
3.4646-3.5311	0.2802	133	0.2622	3427	X-RAY DIFFRACTION	100
3.5311-3.6031	0.2759	147	0.2451	3392	X-RAY DIFFRACTION	100
3.6031-3.6813	0.2979	135	0.2417	3433	X-RAY DIFFRACTION	100
3.6813-3.7668	0.2463	137	0.2298	3413	X-RAY DIFFRACTION	100
3.7668-3.8608	0.2651	164	0.2394	3282	X-RAY DIFFRACTION	97
3.8608-3.965	0.242	132	0.2227	3372	X-RAY DIFFRACTION	99
3.965-4.0814	0.228	144	0.1907	3406	X-RAY DIFFRACTION	100
4.0814-4.2127	0.1708	132	0.1712	3433	X-RAY DIFFRACTION	100
4.2127-4.3629	0.2093	138	0.1651	3417	X-RAY DIFFRACTION	100
4.3629-4.537	0.1896	155	0.1515	3412	X-RAY DIFFRACTION	100
4.537-4.7427	0.2006	136	0.1485	3396	X-RAY DIFFRACTION	100
4.7427-4.9917	0.1925	141	0.1466	3412	X-RAY DIFFRACTION	100
4.9917-5.3028	0.2016	149	0.1619	3427	X-RAY DIFFRACTION	100
5.3028-5.7096	0.1733	138	0.1838	3410	X-RAY DIFFRACTION	100
5.7096-6.2794	0.2671	151	0.198	3406	X-RAY DIFFRACTION	100
6.2794-7.177	0.2211	141	0.1914	3430	X-RAY DIFFRACTION	100
7.177-9.0012	0.1863	148	0.1541	3385	X-RAY DIFFRACTION	100
9.0012-29.8959	0.2216	144	0.1543	3392	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	2.5092	0.0702	-0.1659	4.8099	0.8795	2.7441	0.1756	-0.1629	-0.0302	0.3066	0.0592	-0.2711	0.0589	0.2812	-0.2556	0.6922	-0.0436	-0.0745	0.5413	-0.033	0.646	4.9656	-7.3479	-9.8642
2	2.8588	1.4294	-1.1988	4.0837	-0.2386	2.7319	-0.0699	-0.0791	-0.0354	0.1036	-0.0389	0.1046	0.1367	-0.1393	0.1117	0.6267	0.0018	-0.0238	0.5613	-0.049	0.5432	27.3758	-24.2414	-17.9456
3	3.6071	-0.6955	-0.6605	2.8908	0.232	3.8896	-0.5103	0.4491	-1.1483	-0.1315	-0.0612	0.3669	0.5397	-0.24	0.603	0.5804	-0.0909	0.1758	0.4764	-0.0745	0.8425	20.9914	-41.0101	-20.7047
4	2.2939	1.6826	0.66	4.0841	-0.9806	4.36	0.2113	-0.2668	-0.2105	0.6382	-0.1529	0.3618	0.3645	-0.1574	-0.2343	0.9655	-0.034	0.2017	0.6565	-0.0237	0.8329	12.8436	-45.7473	-4.7456
5	3.671	-0.3313	0.7475	3.1156	-0.2568	3.6416	0.0888	0.187	0.288	0.1029	0.0274	-0.4048	-0.5788	0.6375	-0.111	0.6937	-0.1271	0.0247	0.5888	-0.0912	0.5504	42.0419	-7.5577	-25.2064
6	3.5284	0.4914	0.2119	3.0581	-1.5798	3.2702	0.0528	0.0004	-0.3202	0.3133	-0.1504	-0.3836	0.0991	0.5075	0.1222	0.7106	0.1298	-0.0023	0.9012	0.0012	0.5863	48.8258	-20.4768	-47.8457
7	5.0847	-0.3217	-1.1805	5.6791	0.5397	3.4992	-0.5056	0.1903	-0.9199	0.2262	0.1613	0.5921	0.6652	-0.3416	0.2882	0.5743	0.078	0.0787	0.6926	-0.0986	0.6878	35.8496	-30.2293	-51.4033
8	5.4962	-0.7889	3.2179	6.7528	-4.573	6.9597	-0.279	-0.1589	-1.8495	-0.3689	-0.0733	-0.1474	1.3274	1.4956	0.1338	1.009	0.2554	0.3481	0.8787	0.1693	1.1049	47.095	-44.2159	-41.7949
9	1.9653	-1.185	1.0295	0.6797	-0.6517	0.7624	0.9418	-0.2291	-0.6336	0.3622	0.3372	1.1719	0.276	-0.5395	-1.0827	1.3413	0.2927	0.1911	1.2246	0.4744	1.4608	42.5965	-46.9254	-32.5803
10	2.4247	0.4857	-0.1438	3.4827	0.7508	4.2217	0.1473	0.4035	0.6302	-0.3952	-0.1394	-0.2839	-0.8268	0.0462	0.0276	0.8555	0.0236	0.0937	0.7533	0.0911	0.651	47.6179	-2.035	-63.5257
11	3.8112	-1.1869	0.7871	3.7658	-0.6245	3.0616	0.0996	-0.1291	-0.3536	0.0959	-0.0032	-0.1367	0.2599	0.4513	-0.0677	0.3824	0.0092	0.0205	0.584	-0.0321	0.3536	35.1256	-27.8185	-79.3182
12	2.3834	-0.0098	0.5495	3.9516	0.0213	3.1502	0.1718	0.1751	0.3371	-0.1291	-0.1249	0.137	-0.1746	-0.0783	-0.0439	0.4463	-0.0146	0.0199	0.6079	0.0548	0.5481	14.2913	-4.9478	-90.795
13	2.4541	-1.7508	-0.71	6.0068	-0.5412	2.2156	0.0448	-0.1064	0.116	-0.1517	-0.02	0.0253	-0.1014	-0.0333	-0.0231	0.3555	-0.0645	-0.0099	0.4903	-0.0247	0.4308	-5.4944	-23.1991	-81.0822
14	2.1229	1.2167	-0.3208	5.5563	-0.4412	4.9614	0.1593	-0.6833	-0.0434	1.2116	-0.0859	-0.4048	-0.1702	0.4426	-0.1036	0.5165	-0.034	-0.0507	0.5413	-0.0195	0.4805	-0.9458	-32.4058	-68.1168
15	4.4353	1.12	-3.2431	6.084	-0.3586	4.2333	-0.5308	0.0567	-0.8121	-0.4479	0.0291	-0.8112	0.5032	0.2565	0.4365	0.479	0.0174	-0.0025	0.545	0.0108	0.7211	4.8087	-46.7534	-81.2661
16	4.2446	0.2041	-0.7126	5.0102	0.0553	5.2351	-0.0201	-0.3319	0.5132	0.1935	-0.0428	0.4825	-0.7267	-0.5605	0.0702	0.5396	0.1193	0.02	0.5182	-0.0399	0.6045	-18.3346	-5.7439	-75.3741
17	1.541	-0.4377	1.1268	4.5165	1.3036	4.6102	-0.1452	-0.0569	0.1151	0.2019	-0.1578	0.2648	-0.0404	-0.7835	0.3213	0.4782	-0.1126	-0.0122	0.8121	-0.0634	0.5757	-26.7267	-22.4737	-52.1706
18	2.5595	0.1195	1.0419	3.8677	-0.8036	4.4052	0.0983	0.1126	-0.4795	-0.2414	0.1343	0.2927	0.9533	-0.6049	-0.2505	0.6938	-0.1976	0.0844	0.6868	-0.057	0.6005	-28.3099	-40.2338	-63.0427
19	3.8134	-0.041	0.9699	3.6128	0.1968	3.9372	-0.5544	-0.8962	0.9681	0.3683	-0.0081	0.2509	-0.5513	-0.9578	0.5883	0.7357	0.1612	-0.125	0.8039	-0.249	0.7153	-25.1669	-7.0045	-34.8036
20	2.8428	0.7465	0.2482	4.1104	0.2986	3.1114	0.0078	-0.0808	-0.3294	0.0302	-0.1968	0.0032	0.0938	-0.346	0.1851	0.6882	-0.0306	-0.009	0.617	-0.0498	0.6865	-8.5831	-22.8533	-19.5421
21	3.6595	-0.3462	-0.9368	4.549	0.5026	2.9908	-0.0379	0.5552	-0.7953	-0.2573	0.1522	-0.5836	0.4342	0.1091	-0.1187	0.7052	-0.0613	-0.0356	0.5649	-0.0891	0.8933	-4.121	-35.604	-30.9886
22	7.8006	0.8721	-0.3356	4.4331	0.4617	1.0209	0.2476	0.0208	-1.0169	-0.0298	-0.1588	-0.1021	0.6779	-0.2899	-0.0965	0.9617	-0.1588	0.0926	0.7485	-0.1305	0.9737	-21.6576	-47.169	-30.5653
23	0.3077	-0.158	-0.1595	0.0612	0.1338	1.1954	-0.1701	0.3691	-0.442	-1.2208	-0.4246	0.2836	0.0472	-0.0019	0.4086	1.3131	0.1108	-0.0731	1.0116	-0.1173	1.0402	7.9283	-27.2151	-86.5808
24	-0.0048	0.0026	-0.004	-0.0034	-0.0016	0.003	0.1112	0.0029	0.2684	0.4632	-0.1074	0.398	0.0579	-0.2357	-0.0922	0.8507	0.2919	-0.1271	0.8858	-0.1935	1.1033	-21.5894	-26.1456	-27.084
25	0.0014	-0.0081	-0.0056	-0.0028	0.0038	-0.0004	-0.3101	0.2208	0.3204	-0.1683	0.3079	0.8761	-0.2524	0.0155	0.0354	0.8434	0.0978	-0.0172	0.7464	-0.082	0.8632	-28.4306	-21.6343	-67.4243
26	-0.0037	-0.0063	-0.0003	-0.0115	-0.007	0.0003	0.0259	0.0874	0.2347	-0.5612	0.1948	-0.5525	-0.4113	0.1704	-0.2135	0.9408	-0.2087	0.1796	0.9939	0.0224	0.7939	44.7755	-18.1607	-76.7196
27	0.0068	-0.0015	-0.0017	-0.0032	0.0029	0.0005	0.0604	0.092	0.0955	0.2717	0.1716	-0.1675	0.002	0.0613	-0.1071	1.4976	0.152	0.094	0.861	-0.1735	0.7935	15.4696	-24.9292	-8.1483
28	0.5561	0.492	0.3554	0.4378	0.3046	0.2122	0.2147	0.0615	0.2945	0.5146	0.7158	-1.2033	0.2892	0.3174	-0.6106	0.6361	0.0774	0.1791	1.2616	-0.1347	1.028	46.7802	-24.7341	-35.149

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID -1:100 )	A	-1 - 100
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 101:233 )	A	101 - 233
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 234:309 )	A	234 - 309
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 310:353 )	A	310 - 353
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 1:100 )	B	1 - 100
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 101:185 )	B	101 - 185
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 186:309 )	B	186 - 309
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 310:328 )	B	310 - 328
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 329:353 )	B	329 - 353
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 2:100 )	C	2 - 100
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 101:353 )	C	101 - 353
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID -5:100 )	D	-5 - 100
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 101:202 )	D	101 - 202
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 203:271 )	D	203 - 271
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 272:355 )	D	272 - 355
16	X-RAY DIFFRACTION	16	( CHAIN E AND RESID 1:100 )	E	1 - 100
17	X-RAY DIFFRACTION	17	( CHAIN E AND RESID 101:233 )	E	101 - 233
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 234:353 )	E	234 - 353
19	X-RAY DIFFRACTION	19	( CHAIN F AND RESID 1:100 )	F	1 - 100
20	X-RAY DIFFRACTION	20	( CHAIN F AND RESID 101:202 )	F	101 - 202
21	X-RAY DIFFRACTION	21	( CHAIN F AND RESID 203:307 )	F	203 - 307
22	X-RAY DIFFRACTION	22	( CHAIN F AND RESID 308:353 )	F	308 - 353
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 401:401 )	D	401
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 401:401 )	F	401
25	X-RAY DIFFRACTION	25	( CHAIN E AND RESID 401:401 )	E	401
26	X-RAY DIFFRACTION	26	( CHAIN C AND RESID 401:401 )	C	401
27	X-RAY DIFFRACTION	27	( CHAIN A AND RESID 401:401 )	A	401
28	X-RAY DIFFRACTION	28	( CHAIN B AND RESID 401:401 )	B	401

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