PDB-8sxq: Crystal structure of Sel-1 repeat protein LceB from Legionella pn...

ID or keywords:

Entry

Database: PDB / ID: 8sxq

Title

Crystal structure of Sel-1 repeat protein LceB from Legionella pneumophila

Components

SEL-1 repeat protein

Keywords

UNKNOWN FUNCTION / Type IV secretion system / Legionella pneumophila / Sel-1 repeat protein

Function / homology

Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide-like helical domain superfamily / TPR repeat protein

Function and homology information

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Penner, T.V. / Prehna, G.

Funding support

Canada, 2items

Organization	Grant number	Country
Natural Sciences and Engineering Research Council (NSERC, Canada)	RGPIN-2019-05490	Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)	RGPIN-2018-04968	Canada

Citation

Journal: Protein Sci. / Year: 2024
Title: Structural characterization of the Sel1-like repeat protein LceB from Legionella pneumophila.
Authors: Penner, T.V. / Lorente Cobo, N. / Patel, D.T. / Patel, D.H. / Savchenko, A. / Brassinga, A.K.C. / Prehna, G.

History

Deposition	May 23, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 24, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8sxq.cif.gz	587.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8sxq_validation.pdf.gz	463.1 KB	Display	wwPDB validaton report
Full document	8sxq_full_validation.pdf.gz	472.9 KB	Display
Data in XML	8sxq_validation.xml.gz	35.8 KB	Display
Data in CIF	8sxq_validation.cif.gz	48.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sx/8sxq ftp://data.pdbj.org/pub/pdb/validation_reports/sx/8sxq	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&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 (1)

Deposited unit

A: SEL-1 repeat protein

B: SEL-1 repeat protein

C: SEL-1 repeat protein

hetero molecules

127 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SEL-1 repeat protein

hetero molecules

defined by author&software
Evidence: gel filtration
42.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SEL-1 repeat protein

hetero molecules

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

3

C: SEL-1 repeat protein

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

Unit cell

Length a, b, c (Å)	116.790, 116.790, 88.350
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	SEL-1 repeat protein / TPR repeat protein Mass: 42108.758 Da / Num. of mol.: 3 / Mutation: A21M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg1356 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: Q5ZVT4
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.68 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 7mg/mL 0.1M Citric Acid pH 4.0 10% MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18082 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.18082 Å / Relative weight: 1
Reflection	Resolution: 2.7→48.72 Å / Num. obs: 36977 / % possible obs: 99.91 % / Redundancy: 4.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.021 / Net I/σ(I): 20.5
Reflection shell	Resolution: 2.7→2.797 Å / Num. unique obs: 3696 / CC_1/2: 0.499

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→48.72 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2508	1849	5 %
R_work	0.2173	-	-
obs	0.219	36977	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→48.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8210	0	24	48	8282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	13.702	3024
X-RAY DIFFRACTION	f_chiral_restr	0.032	1116
X-RAY DIFFRACTION	f_plane_restr	0.002	1484

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 (%)
2.7-2.77	0.3301	141	0.3313	2692	X-RAY DIFFRACTION	100
2.77-2.85	0.3949	144	0.3218	2724	X-RAY DIFFRACTION	100
2.85-2.95	0.3746	142	0.364	2699	X-RAY DIFFRACTION	100
2.95-3.05	0.4278	142	0.3785	2701	X-RAY DIFFRACTION	100
3.05-3.17	0.3718	141	0.3046	2682	X-RAY DIFFRACTION	100
3.17-3.32	0.2923	144	0.2646	2732	X-RAY DIFFRACTION	100
3.32-3.49	0.2871	141	0.2568	2686	X-RAY DIFFRACTION	100
3.49-3.71	0.2857	143	0.2654	2710	X-RAY DIFFRACTION	100
3.71-4	0.2282	142	0.2218	2698	X-RAY DIFFRACTION	100
4-4.4	0.2621	143	0.2021	2722	X-RAY DIFFRACTION	100
4.4-5.03	0.2147	142	0.1875	2703	X-RAY DIFFRACTION	100
5.04-6.34	0.2431	142	0.2062	2688	X-RAY DIFFRACTION	100
6.34-48.72	0.198	142	0.1661	2691	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	2.3941	-0.9992	2.7083	1.1952	-0.5238	7.3883	-0.1872	0.0565	0.3211	-0.0413	0.1074	-0.1061	-0.6469	-0.1254	0.0997	0.7647	-0.0413	-0.0708	0.6462	0.0119	0.8753	24.1381	30.9921	13.7189
2	6.4469	0.7828	4.7618	2.2062	-1.2304	9.2658	-0.244	0.4503	-0.1792	0.154	-0.0133	-0.3109	-0.5955	-0.2656	0.2459	0.6364	-0.0228	0.0097	0.8739	0.0228	0.8057	15.2648	25.3041	-7.0248
3	7.6862	0.8071	-2.1718	2.2483	-0.5729	0.5542	-0.0552	-0.1026	-1.2205	0.1019	-0.0684	-0.2553	0.2175	0.1556	-0.1044	0.7565	-0.1022	-0.09	0.8847	-0.0398	1.0479	5.1011	9.8174	-7.6049
4	7.6449	-1.4343	-0.5275	1.6678	0.2822	1.6633	0.1889	-0.9949	-0.5565	0.5685	-0.1018	-0.2851	-0.1005	0.0968	-0.0829	0.8434	-0.1962	-0.0955	0.8744	0.1116	0.8943	-17.258	13.4524	2.6733
5	9.4536	1.3908	1.2316	7.3263	-1.2579	5.8916	-0.0315	0.5622	0.6472	-0.4797	0.2229	0.296	-0.1875	-0.4794	-0.1229	0.8536	-0.0359	0.103	0.715	0.1246	0.9255	-28.7346	27.29	-6.2076
6	1.355	0.253	0.5227	6.6631	-0.5805	2.3956	1.3671	-0.1063	0.9447	-0.3494	-0.7902	-0.4101	-0.9864	0.7579	-0.485	1.1482	-0.3269	0.1749	0.8345	0.1132	1.2124	-25.416	36.5153	-2.5234
7	3.4462	0.1575	-1.0062	3.6615	1.8976	8.4957	0.2494	-0.1201	0.0178	0.2981	-0.353	0.4036	-0.0149	-0.6773	0.1506	0.8297	-0.0619	0.1127	0.8353	-0.0435	0.8563	-41.4601	57.7488	-10.6201
8	4.4404	-0.2909	-0.3971	2.1046	0.6049	7.2169	0.0948	0.5929	0.2486	-0.1025	-0.3033	-0.0459	0.4691	-0.047	0.1778	0.739	0.1377	0.0186	0.7055	0.0106	0.8169	-29.3762	52.0733	-31.6822
9	5.2432	-1.8005	-0.8071	2.9532	1.4763	6.2012	0.0608	0.9717	1.2791	-0.5754	-0.0915	-0.6569	-0.9953	0.7071	0.0506	0.766	0.0096	0.1047	1.0623	0.2967	1.3051	-12.1743	60.0045	-37.9821
10	1.8197	-2.9229	-0.0099	3.3048	-0.8093	1.5322	-0.0499	-0.0398	0.4333	0.1563	0.1272	-0.2965	-0.0707	-0.0311	-0.0408	0.6989	-0.0378	-0.0069	1.099	0.0182	1.0244	6.3064	44.4803	-28.5787
11	6.7459	-3.4626	0.4219	8.5658	-2.6013	3.8978	0.2992	0.8602	-0.3162	-1.3515	-0.3488	0.3907	0.6671	-0.5486	0.001	1.0649	-0.0894	-0.0902	1.0778	-0.1526	0.9378	6.6966	23.1254	-34.7468
12	-1.1496	-0.1563	-0.346	1.1159	0.1686	0.4358	-0.277	0.5847	-0.2867	-0.1267	-0.4563	0.1454	-0.1047	-1.3499	0.6413	0.934	-0.0078	-0.1792	1.9097	-0.5694	1.3279	37.7525	8.1088	-16.1795
13	3.0369	-3.1335	2.2616	5.7092	1.0167	3.1577	0.3034	0.5622	0.5673	0.0836	-0.6139	-0.8731	0.3257	0.2992	0.3102	0.8905	-0.0935	-0.1278	0.9297	0.3269	1.0262	40.0259	44.0602	-10.4606
14	5.5574	2.1918	0.7891	4.3304	3.0842	2.784	-0.7883	-2.4906	0.9851	2.0893	0.6436	1.3803	1.1703	-1.4689	0.431	1.2925	0.1287	-0.0418	1.939	0.0095	1.4162	17.4285	50.3551	-6.1286

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 120 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 121 through 156 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 157 through 229 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 230 through 316 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 317 through 352 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 353 through 369 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 21 through 86 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 87 through 171 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 172 through 206 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 207 through 336 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 337 through 368 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 21 through 192 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 193 through 347 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 348 through 371 )

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