PDB-5fia: Structure of the effector protein LpiR1 (Lpg0634) from Legionella...

ID or keywords:

Entry

Database: PDB / ID: 5fia

Title

Structure of the effector protein LpiR1 (Lpg0634) from Legionella pneumophila

Components

LpiR1

Keywords

SIGNALING PROTEIN /

Legionella pneumophila /

bacterial effector / internal repeat

Function / homology

Putative substrate of the Dot/Icm secretion system superfamily / Putative substrate of the Dot/Icm secretion system / Substrate of the Dot/Icm secretion system, putative / : /

Type IV secretion protein Dot

Function and homology information

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Beyrakhova, K. / van Straaten, K. / Cygler, M.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Investigations of the Effector Protein LpiR1 from Legionella pneumophila.
Authors: Beyrakhova, K.A. / van Straaten, K. / Li, L. / Boniecki, M.T. / Anderson, D.H. / Cygler, M.

History

Deposition	Dec 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2016	Group: Database references
Revision 1.2	Aug 3, 2016	Group: Database references
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5fia.cif.gz	337.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5fia.ent.gz	275.1 KB	Display	PDB format
PDBx/mmJSON format	5fia.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/5fia ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fia	HTTPS FTP

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Related structure data

Related structure data	5jg4C C: citing same article (ref.)
Similar structure data	5es2-2 4pgc-1 1dcl-d 2q7y-2 1mcb-d 2yhx-d 5thk-2 4ono-d 2clz-1 4jax-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LpiR1

B: LpiR1

hetero molecules

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

1

A: LpiR1

hetero molecules

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

2

B: LpiR1

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.420, 71.820, 94.180
Angle α, β, γ (deg.)	90.00, 111.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	LpiR1 Mass: 45640.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia-1 / Gene: lpymg_00644 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C9P234, UniProt: Q5ZXU7*PLUS
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0, MPD 40%

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 11, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. obs: 100375 / % possible obs: 98.7 % / Redundancy: 4.6 % / Net I/σ(I): 17.39
Reflection shell	Resolution: 1.75→1.8 Å / R_merge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→48.805 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1901	5086	5.07 %
R_work	0.162	-	-
obs	0.1634	100369	98.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→48.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6232	0	44	632	6908

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6395
X-RAY DIFFRACTION	f_angle_d	0.848	8612
X-RAY DIFFRACTION	f_dihedral_angle_d	14.286	4017
X-RAY DIFFRACTION	f_chiral_restr	0.05	991
X-RAY DIFFRACTION	f_plane_restr	0.005	1102

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 (%)
1.7501-1.7699	0.3142	198	0.2796	3139	X-RAY DIFFRACTION	98
1.7699-1.7908	0.2905	172	0.2651	3075	X-RAY DIFFRACTION	98
1.7908-1.8126	0.3108	175	0.2506	3143	X-RAY DIFFRACTION	98
1.8126-1.8356	0.3085	176	0.2443	3108	X-RAY DIFFRACTION	98
1.8356-1.8597	0.2882	158	0.2228	3128	X-RAY DIFFRACTION	98
1.8597-1.8852	0.2306	170	0.2011	3187	X-RAY DIFFRACTION	98
1.8852-1.9121	0.2418	171	0.1997	3128	X-RAY DIFFRACTION	98
1.9121-1.9407	0.198	157	0.1916	3180	X-RAY DIFFRACTION	98
1.9407-1.971	0.1974	142	0.1778	3127	X-RAY DIFFRACTION	98
1.971-2.0033	0.2086	151	0.1749	3196	X-RAY DIFFRACTION	99
2.0033-2.0378	0.2155	149	0.1704	3172	X-RAY DIFFRACTION	99
2.0378-2.0749	0.2089	193	0.1719	3097	X-RAY DIFFRACTION	98
2.0749-2.1148	0.1882	169	0.1633	3155	X-RAY DIFFRACTION	98
2.1148-2.158	0.2163	176	0.1595	3143	X-RAY DIFFRACTION	99
2.158-2.2049	0.1896	169	0.1528	3177	X-RAY DIFFRACTION	99
2.2049-2.2562	0.1894	182	0.1551	3162	X-RAY DIFFRACTION	99
2.2562-2.3126	0.1953	161	0.1531	3189	X-RAY DIFFRACTION	99
2.3126-2.3751	0.1593	146	0.1543	3175	X-RAY DIFFRACTION	99
2.3751-2.445	0.197	189	0.1602	3141	X-RAY DIFFRACTION	99
2.445-2.5239	0.186	165	0.161	3236	X-RAY DIFFRACTION	99
2.5239-2.6141	0.1967	167	0.1592	3166	X-RAY DIFFRACTION	99
2.6141-2.7188	0.1753	173	0.1597	3195	X-RAY DIFFRACTION	99
2.7188-2.8425	0.1887	170	0.1602	3198	X-RAY DIFFRACTION	99
2.8425-2.9924	0.1931	177	0.1679	3205	X-RAY DIFFRACTION	99
2.9924-3.1798	0.2092	175	0.1614	3203	X-RAY DIFFRACTION	100
3.1798-3.4253	0.1749	178	0.1579	3206	X-RAY DIFFRACTION	100
3.4253-3.7699	0.1973	166	0.1486	3230	X-RAY DIFFRACTION	100
3.7699-4.3151	0.146	155	0.1369	3247	X-RAY DIFFRACTION	100
4.3151-5.4354	0.1671	168	0.1472	3270	X-RAY DIFFRACTION	100
5.4354-48.8241	0.1807	188	0.1685	3305	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	1.9029	-0.3045	-0.2282	1.9815	0.044	2.5711	-0.0211	-0.2885	0.0974	0.1708	0.0734	-0.2379	-0.2141	0.4554	-0.0312	0.2776	-0.0475	-0.0046	0.4207	-0.031	0.2292	12.8845	22.6862	47.9689
2	3.4368	0.8132	-0.1386	3.0623	0.4287	2.6143	-0.2087	-0.3338	-0.3554	0.1671	0.1007	-0.607	0.4294	0.8559	0.1238	0.3184	0.1009	-0.0286	0.6822	0.0578	0.3771	21.5023	10.9192	48.992
3	1.7586	-0.3566	-0.0083	1.4493	-0.4042	2.9315	-0.0734	-0.1211	0.1681	-0.1172	0.0945	0.0939	-0.2039	-0.0042	-0.0362	0.2232	-0.02	0.0084	0.251	-0.0133	0.2262	5.5579	23.1179	34.7258
4	2.1549	1.7421	0.4783	8.4311	0.5838	1.96	-0.0177	-0.1886	-0.161	0.0495	0.1128	-0.2494	0.0616	0.154	-0.1475	0.2335	-0.0104	0.0121	0.3103	0.0144	0.2188	11.9322	12.4716	32.6957
5	1.0106	0.0936	0.3002	3.3545	-0.3903	1.9195	0.0727	-0.1871	-0.0639	0.1463	0.1987	1.1056	-0.1583	-0.6374	-0.1251	0.3537	-0.0542	0.037	0.5422	0.1222	0.6566	-10.5045	6.9145	23.8929
6	1.833	-0.3331	0.0668	3.9598	0.8663	2.574	0.1072	0.3342	-0.5039	-1.056	0.2974	0.305	0.2645	0.028	-0.1189	0.6755	-0.0674	-0.2851	0.5395	-0.0841	0.5793	-4.5013	-0.9007	3.1446
7	7.3954	-2.6508	-2.4143	2.0496	1.4394	2.4913	0.0454	-0.0873	-0.4985	-0.3373	0.1649	0.808	0.0729	-0.6286	-0.0552	0.3552	-0.1165	-0.1362	0.4858	0.111	0.6563	-9.55	0.1315	15.5379
8	2.1909	-0.1905	0.6085	3.7395	0.4774	2.0931	0.0783	0.0307	-0.2367	-0.2551	0.048	0.4009	0.1619	-0.2409	-0.1133	0.2246	-0.055	-0.0459	0.2261	0.0387	0.256	-0.1058	4.7978	18.2941
9	1.6944	0.9835	0.4566	6.5496	0.6087	1.8029	-0.1454	0.137	0.1752	-0.3117	0.2394	-0.2726	-0.3733	0.2078	-0.0893	0.263	-0.0644	0.0367	0.2706	0.0166	0.2297	10.7391	20.523	23.9104
10	2.3219	0.5238	-0.2959	1.8299	-0.1101	1.9041	0.1006	0.3396	-0.2488	-0.1428	-0.0718	0.126	0.2623	-0.0977	-0.0706	0.2553	0.0349	-0.0278	0.2617	-0.0588	0.2095	-13.2206	3.5063	61.1775
11	1.7916	-0.0111	0.2658	1.0529	0.1355	1.6886	0.0642	0.094	-0.1653	0.0248	-0.0529	-0.0516	0.2093	-0.0929	0.0182	0.1936	-0.0082	-0.0021	0.1284	-0.0187	0.1804	-11.6189	5.4542	72.0676
12	1.2961	-0.0468	0.2953	2.1403	0.4595	1.0201	0.0826	0.243	0.2245	-0.2267	-0.1406	-0.1182	-0.1454	-0.0303	0.0666	0.2716	-0.025	0.0031	0.2189	0.0225	0.3161	0.0222	27.3147	84.9667
13	1.7051	0.6589	0.486	1.3206	0.4868	1.505	0.121	-0.1963	-0.0309	0.1612	-0.139	-0.06	0.0973	-0.111	0.0317	0.2058	-0.034	0.0081	0.1524	0.0065	0.1914	-5.0159	20.0861	92.7065

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 89 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 90 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 181 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 182 through 211 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 212 through 239 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 265 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 266 through 365 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 366 through 401 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 181 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 182 through 211 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 212 through 401 )

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