PDB-5tsc: The crystal structure of Lpg2147 from Legionella pneumophila

ID or keywords:

Entry

Database: PDB / ID: 5tsc

Title

The crystal structure of Lpg2147 from Legionella pneumophila

Components

Uncharacterized protein

Keywords

UNKNOWN FUNCTION / Midwest center for structural genomics / MCSG / PSI-Biology

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.008 Å

Authors

Valleau, D. / Xu, X. / Cui, H. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM07492	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094585	United States

Citation

Journal: To Be Published
Title: The crystal structure of Lpg2147 from Legionella pneumophila
Authors: Valleau, D.

History

Deposition	Oct 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 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	5tsc.cif.gz	328.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5tsc.ent.gz	268.4 KB	Display	PDB format
PDBx/mmJSON format	5tsc.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/ts/5tsc ftp://data.pdbj.org/pub/pdb/validation_reports/ts/5tsc	HTTPS FTP

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Related structure data

Related structure data	5sujS S: Starting model for refinement
Similar structure data	5w0z-2 3u28-d 3s1j-d 7kn5-1 5w0u-2 4iao-2 4j9z-d 3ubc-d 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC108142

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

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

1

A: Uncharacterized protein

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

2

B: Uncharacterized protein

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

Unit cell

Length a, b, c (Å)	48.927, 68.373, 71.655
Angle α, β, γ (deg.)	117.13, 98.77, 90.28
Int Tables number	1
Space group name H-M	P1

#1: Protein	Uncharacterized protein Mass: 52786.754 Da / Num. of mol.: 2 / Fragment: residues 1-462 / Mutation: C74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2147 / Plasmid: p15TV-l / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q5ZTL4
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uncharacterized protein

Mass: 52786.754 Da / Num. of mol.: 2 / Fragment: residues 1-462 / Mutation: C74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2147 / Plasmid: p15TV-l / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q5ZTL4

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 465 / 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: 1.99 Å³/Da / Density % sol: 38.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1 M bis-tris ph 5.5, 0.2 M MgCl2, 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97915 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2014
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.008→50 Å / Num. obs: 52808 / % possible obs: 97.6 % / Redundancy: 2.2 % / R_merge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.008→2.03 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.314 / Mean I/σ(I) obs: 3.33 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1-2155_1496)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5SUJ

5suj

Resolution: 2.008→36.025 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 21.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2104	1943	3.85 %	Random selection
R_work	0.1739	-	-	-
obs	0.1753	50531	93.03 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.008→36.025 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6048	0	0	465	6513

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6191
X-RAY DIFFRACTION	f_angle_d	0.702	8358
X-RAY DIFFRACTION	f_dihedral_angle_d	15.936	2364
X-RAY DIFFRACTION	f_chiral_restr	0.049	915
X-RAY DIFFRACTION	f_plane_restr	0.004	1085

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 (%)
2.0083-2.0585	0.2469	114	0.209	2618	X-RAY DIFFRACTION	71
2.0585-2.1142	0.256	134	0.2087	3203	X-RAY DIFFRACTION	86
2.1142-2.1764	0.2498	135	0.1961	3349	X-RAY DIFFRACTION	90
2.1764-2.2466	0.2379	130	0.1916	3442	X-RAY DIFFRACTION	92
2.2466-2.3269	0.202	143	0.1826	3471	X-RAY DIFFRACTION	93
2.3269-2.42	0.2051	129	0.1836	3535	X-RAY DIFFRACTION	95
2.42-2.5301	0.2425	142	0.1851	3538	X-RAY DIFFRACTION	95
2.5301-2.6635	0.2431	138	0.1879	3583	X-RAY DIFFRACTION	96
2.6635-2.8303	0.2376	146	0.1894	3626	X-RAY DIFFRACTION	97
2.8303-3.0487	0.2532	144	0.19	3663	X-RAY DIFFRACTION	98
3.0487-3.3553	0.1981	149	0.176	3652	X-RAY DIFFRACTION	98
3.3553-3.8404	0.2027	145	0.1596	3690	X-RAY DIFFRACTION	98
3.8404-4.8366	0.1496	149	0.1387	3672	X-RAY DIFFRACTION	99
4.8366-36.0309	0.2015	145	0.1645	3546	X-RAY DIFFRACTION	95

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	4.296	-0.4951	0.0268	2.1606	0.7564	6.1202	0.3779	0.6784	0.2644	-0.8143	-0.2964	0.2266	-0.8436	-0.6229	0.0373	0.2625	0.0956	-0.0228	0.2223	0.036	0.1866	19.6495	66.4062	-20.1762
2	8.5264	3.7324	-5.7818	2.9985	-2.696	3.9476	0.0339	0.101	-0.0743	-0.1636	-0.0263	0.0222	-0.1219	-0.1315	-0.0295	0.1129	0.025	-0.0423	0.117	-0.0112	0.1237	7.1729	65.309	-2.2808
3	7.0066	-5.7141	-5.4559	7.3953	5.2645	4.8572	-0.0502	-0.7002	0.4044	-0.0646	0.298	-0.2704	-0.6384	0.8392	-0.2857	0.2326	-0.0212	-0.0054	0.253	0.0163	0.2043	4.2115	68.6784	19.0089
4	2.8831	-1.7244	-4.553	2.4086	2.1341	7.1207	0.4361	-0.7697	0.2539	0.2795	0.2047	-0.7339	-0.4656	1.1993	-0.6003	0.1936	-0.0838	-0.0001	0.3029	-0.0474	0.2389	10.6986	70.2812	9.3474
5	0.5609	1.1982	1.2152	6.8893	2.6597	2.7368	0.0982	-0.426	-0.1376	-0.0652	0.0237	0.6287	0.0335	-0.6462	0.0962	0.0878	0.0049	0.0065	0.2392	0.0134	0.1789	18.9731	56.1051	-7.0302
6	6.5018	-2.0745	4.1585	4.8375	-1.6092	3.1103	0.3561	0.0558	-1.4393	-0.2218	0.0384	0.7892	0.4353	-0.2257	-0.3388	0.2374	-0.0148	-0.0078	0.1733	0.0035	0.2566	23.4046	46.7767	-14.3465
7	3.6793	-1.6723	1.6354	2.2299	-0.7762	4.5927	0.1962	-0.1756	-0.3835	-0.0932	0.0333	0.1255	0.2174	-0.0386	-0.1482	0.139	0.0268	-0.0038	0.0977	-0.0189	0.1478	32.3503	49.4655	-13.348
8	4.9174	0.6195	1.8073	5.1618	0.8959	4.7532	0.0564	0.2388	-0.5156	0.0954	0.0279	-0.033	0.3371	0.1109	-0.0344	0.206	-0.0519	0.0023	0.1294	-0.0188	0.233	41.7678	35.8685	20.7456
9	5.654	-1.5453	1.8785	3.2153	-0.052	5.0196	-0.0541	1.8224	0.5107	-2.4253	-0.5483	1.5476	0.5301	-0.4099	0.5445	0.8213	0.0122	-0.2019	0.6757	-0.1515	0.563	40.6759	32.496	5.168
10	4.9533	-1.1884	1.6385	4.1321	0.6287	4.2787	0.0572	0.2049	0.0049	-0.2731	-0.0628	-0.2407	-0.2513	0.1948	0.1524	0.0421	-0.0059	0.0236	0.059	-0.0498	0.1201	30.9583	55.0416	-15.5119
11	2.9662	-0.7482	-1.5446	2.5276	2.8494	5.7556	0.0813	-0.1828	0.2762	-0.2608	-0.1181	-0.2506	-0.3744	-0.0826	-0.1195	0.1155	0.0301	0.0317	0.1513	-0.0197	0.0622	27.9945	64.0936	-8.6838
12	5.0144	-3.0708	3.7257	6.0623	-5.9797	7.8392	0.039	-0.084	0.5552	-0.3584	-0.3077	-0.9601	0.2754	0.4748	0.2103	0.1198	0.0253	0.0355	0.171	-0.0436	0.1929	41.4202	56.4401	-11.5264
13	3.9191	0.4734	2.168	2.8361	0.4837	3.3449	-0.0263	-0.3674	0.0929	0.3175	-0.0496	-0.1497	-0.1362	0.1281	0.0628	0.0741	-0.0035	0.0248	0.1885	0.0029	0.1102	36.3128	56.9561	-3.0625
14	4.1441	-4.7509	-2.6806	7.912	6.0748	6.4379	0.3711	0.5477	-0.227	-0.397	-0.3875	0.3806	-0.2314	-0.456	0.6795	0.1807	0.0429	-0.0677	0.179	-0.001	0.2145	8.0985	64.4674	-17.3348
15	6.7253	-2.0062	0.3208	7.9561	-5.8059	8.6371	-0.0851	0.1003	1.0499	-0.0106	-0.0157	-0.584	-0.5694	0.3906	0.1271	0.2181	0.0077	0.047	0.1091	-0.0092	0.2484	8.8283	78.0374	-8.5139
16	4.6096	0.0883	-2.2059	7.083	-1.173	6.1729	0.4638	-0.6055	0.1346	0.5215	-0.0404	0.5527	-0.4147	-0.8169	-0.3861	0.1315	-0.0179	0.035	0.3445	-0.0233	0.1609	-0.2736	69.4501	9.0537
17	7.1161	-0.4012	-3.4073	3.0947	0.749	3.3469	-0.0492	-0.5489	-0.0027	0.3264	0.1041	0.0987	-0.0986	0.2815	-0.0627	0.1265	0.0167	-0.0023	0.0985	0.0092	0.0966	8.7485	85.9698	-20.3002
18	3.1345	2.7837	-4.7522	5.0922	-3.7808	7.9069	0.1849	0.1988	-0.0256	-0.1793	-0.0158	-0.2808	-0.1512	0.1492	-0.196	0.1322	0.0083	0.0325	0.1866	0.0017	0.1427	26.682	91.0356	-46.5266
19	8.1744	-2.4489	-3.208	0.7889	0.5254	2.506	-0.166	-0.0257	0.2313	-0.0315	0.076	-0.1719	-0.1014	0.166	0.033	0.2126	-0.0222	0.0195	0.1305	-0.056	0.178	14.6607	94.048	-35.1483
20	6.6111	-4.1478	2.4479	6.4153	-1.6987	4.4374	0.0524	0.6684	-0.1841	-0.6195	-0.209	0.3213	0.565	0.165	0.1043	0.2257	-0.041	-0.0013	0.1794	-0.0488	0.2374	-5.7245	85.6525	-31.3912
21	3.7111	-1.9965	0.3805	5.818	-2.5592	3.2897	0.0794	-0.2036	0.0239	-0.0643	0.2591	0.9672	-0.0588	-0.3093	-0.2277	0.1049	-0.0191	0.0181	0.1434	-0.0398	0.2867	-12.1881	94.7892	-22.6131
22	1.579	-0.6505	0.7494	0.4164	-0.5765	0.9283	-0.3302	0.8487	-0.43	-1.3774	0.5554	-0.3305	0.3134	0.6394	-0.0808	0.9148	-0.2449	-0.0374	0.4869	-0.0941	0.3368	-8.3685	115.1367	-52.7256
23	6.126	1.6054	2.0693	2.7757	0.379	8.9052	-0.5593	0.9271	-0.9727	-1.6688	0.6196	-0.356	0.3632	0.7401	-0.518	0.9969	-0.431	-0.0663	0.6001	-0.2971	0.3069	-7.6852	111.4589	-57.5316
24	0.409	-0.0798	-0.2612	0.128	0.0039	0.1808	-0.4711	0.57	0.2919	-0.5838	0.0186	0.2483	-0.3087	-0.1508	-0.1213	1.5057	-0.5558	-1.2998	0.9512	0.1752	0.9498	-20.6298	117.0244	-61.9504
25	3.6716	2.6488	-1.1129	2.027	-0.948	4.255	-0.4754	0.9634	1.8132	-1.5567	0.906	1.7864	-0.6374	-0.859	-0.226	0.8443	-0.278	-0.3197	0.4677	0.2334	0.9742	-14.4226	129.3401	-52.9571
26	3.4489	-2.8495	4.2933	4.7882	-5.324	6.8875	0.0277	0.1915	0.1775	-0.4923	0.2214	0.9346	0.0808	-0.2162	-0.356	0.3099	-0.0342	-0.1405	0.2067	0.036	0.4896	-12.8289	107.3843	-41.3257
27	2.8246	-2.1996	3.1154	4.6241	-3.6525	3.9624	-0.6982	-1.4539	-0.3856	1.8412	-0.0749	0.6634	-0.2094	-0.5931	-0.149	0.4614	-0.0332	0.2493	0.4291	0.1015	0.3659	-8.2837	90.6422	-9.5142
28	3.1276	-1.465	-0.3889	2.716	-0.1573	1.294	-0.0516	-0.1627	0.0817	0.1202	0.0096	0.1	-0.1454	0.0394	0.0498	0.1119	-0.0255	0.0151	0.0706	-0.0566	0.1149	-0.8102	103.462	-22.8071
29	2.9839	-1.5694	0.7512	3.0783	-0.3639	1.8227	-0.0699	-0.0075	0.4096	-0.1161	-0.0123	-0.0472	-0.2127	0.0464	0.0995	0.1356	0.0042	0.0533	0.0978	-0.0601	0.13	-1.7991	102.3066	-27.0611
30	7.0696	-2.9022	-3.7244	1.425	1.5747	6.1186	-0.2703	-0.0718	-0.547	0.0258	-0.0503	0.1663	0.5157	0.1601	0.2655	0.2041	0.0109	-0.0041	0.0928	0.0367	0.2006	13.2652	77.2202	-24.461
31	2.0191	0.6082	-1.0041	3.9155	-1.8434	6.3511	-0.0298	-0.3295	0.0172	0.0024	0.0702	-0.3499	0.2259	0.8592	0.0076	0.0631	0.0353	-0.0064	0.2493	-0.0077	0.1507	25.6833	84.8466	-32.0059
32	6.0396	-4.7926	6.6743	9.3658	-3.1373	8.206	-0.9862	1.2542	-1.5148	-1.4684	-0.1423	0.0669	1.8333	0.2799	0.9622	0.7655	-0.1402	0.2843	0.3911	-0.0796	0.4847	29.2778	84.1596	-53.7248

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 7:22)
2	X-RAY DIFFRACTION	2	(chain A and resid 23:41)
3	X-RAY DIFFRACTION	3	(chain A and resid 42:56)
4	X-RAY DIFFRACTION	4	(chain A and resid 57:71)
5	X-RAY DIFFRACTION	5	(chain A and resid 72:83)
6	X-RAY DIFFRACTION	6	(chain A and resid 84:105)
7	X-RAY DIFFRACTION	7	(chain A and resid 106:129)
8	X-RAY DIFFRACTION	8	(chain A and resid 130:217)
9	X-RAY DIFFRACTION	9	(chain A and resid 218:225)
10	X-RAY DIFFRACTION	10	(chain A and resid 226:245)
11	X-RAY DIFFRACTION	11	(chain A and resid 246:272)
12	X-RAY DIFFRACTION	12	(chain A and resid 273:292)
13	X-RAY DIFFRACTION	13	(chain A and resid 293:334)
14	X-RAY DIFFRACTION	14	(chain A and resid 335:353)
15	X-RAY DIFFRACTION	15	(chain A and resid 354:364)
16	X-RAY DIFFRACTION	16	(chain A and resid 365:384)
17	X-RAY DIFFRACTION	17	(chain B and resid 7:33)
18	X-RAY DIFFRACTION	18	(chain B and resid 34:61)
19	X-RAY DIFFRACTION	19	(chain B and resid 62:79)
20	X-RAY DIFFRACTION	20	(chain B and resid 80:101)
21	X-RAY DIFFRACTION	21	(chain B and resid 102:124)
22	X-RAY DIFFRACTION	22	(chain B and resid 125:139)
23	X-RAY DIFFRACTION	23	(chain B and resid 140:168)
24	X-RAY DIFFRACTION	24	(chain B and resid 169:180)
25	X-RAY DIFFRACTION	25	(chain B and resid 181:211)
26	X-RAY DIFFRACTION	26	(chain B and resid 212:236)
27	X-RAY DIFFRACTION	27	(chain B and resid 237:247)
28	X-RAY DIFFRACTION	28	(chain B and resid 248:299)
29	X-RAY DIFFRACTION	29	(chain B and resid 300:339)
30	X-RAY DIFFRACTION	30	(chain B and resid 340:353)
31	X-RAY DIFFRACTION	31	(chain B and resid 354:378)
32	X-RAY DIFFRACTION	32	(chain B and resid 379:384)

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