PDB-8v1k: Crystal structure of outer membrane lipoprotein carrier protein (...

ID or keywords:

Entry

Database: PDB / ID: 8v1k

Title

Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella tularensis

Components

Outer-membrane lipoprotein carrier protein

Keywords

LIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / LolA

Function / homology

Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / lipoprotein transport / periplasmic space / Outer-membrane lipoprotein carrier protein

Function and homology information

Biological species

Francisella tularensis subsp. tularensis SCHU S4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Francisella tularensis
Authors: Lovell, S. / Woodward, E.L. / Cooper, A. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Nov 20, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 29, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8v1k.cif.gz	169.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8v1k.ent.gz	132.5 KB	Display	PDB format
PDBx/mmJSON format	8v1k.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8v1k_validation.pdf.gz	454.1 KB	Display	wwPDB validaton report
Full document	8v1k_full_validation.pdf.gz	456.7 KB	Display
Data in XML	8v1k_validation.xml.gz	17.4 KB	Display
Data in CIF	8v1k_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v1/8v1k ftp://data.pdbj.org/pub/pdb/validation_reports/v1/8v1k	HTTPS FTP

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Related structure data

Similar structure data	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

Deposited unit

A: Outer-membrane lipoprotein carrier protein

B: Outer-membrane lipoprotein carrier protein

hetero molecules

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

1

A: Outer-membrane lipoprotein carrier protein

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

2

B: Outer-membrane lipoprotein carrier protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.809, 84.550, 102.469
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Outer-membrane lipoprotein carrier protein Mass: 23821.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria) Gene: lolA / Plasmid: FrtuB.17730.a.VM3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5NEJ3
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.91 Å³/Da / Density % sol: 35.43 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus Fusion H10: 12.5% v/v MPD; 12.5% PEG 1000; 25%w/v PEG 3350, 0.05M Tris (base), 0.05M BICINE, 0.3% w/v Sodium-L ascorbate, 0.3% w/v Choline Chloride, 0.3% v/v D-Panthenol, 0.3% w/v ...Details: Morpheus Fusion H10: 12.5% v/v MPD; 12.5% PEG 1000; 25%w/v PEG 3350, 0.05M Tris (base), 0.05M BICINE, 0.3% w/v Sodium-L ascorbate, 0.3% w/v Choline Chloride, 0.3% v/v D-Panthenol, 0.3% w/v Pyridoxine hydrochloride, 0.3% w/v Thiamine hydrochloride, FrtuB.17730.a.VM3.PB00127 at 6.2 mg/mL. Plate 13568 well H10 drop2. Puck: PSL-1012, Cryo: direct

Crystal

Density Matthews: 1.91 Å³/Da / Density % sol: 35.43 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus Fusion H10: 12.5% v/v MPD; 12.5% PEG 1000; 25%w/v PEG 3350, 0.05M Tris (base), 0.05M BICINE, 0.3% w/v Sodium-L ascorbate, 0.3% w/v Choline Chloride, 0.3% v/v D-Panthenol, 0.3% w/v ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→42.28 Å / Num. obs: 34082 / % possible obs: 100 % / Redundancy: 6.9 % / CC_1/2: 0.996 / R_merge(I) obs: 0.094 / R_pim(I) all: 0.039 / R_rim(I) all: 0.102 / Χ²: 0.86 / Net I/σ(I): 9.2 / Num. measured all: 235202
Reflection shell	Resolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 6.7 % / R_merge(I) obs: 0.894 / Num. measured all: 13173 / Num. unique obs: 1980 / CC_1/2: 0.754 / R_pim(I) all: 0.374 / R_rim(I) all: 0.97 / Χ²: 0.65 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5150: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→26.53 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2354	1621	4.76 %
R_work	0.1989	-	-
obs	0.2006	34021	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→26.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2966	0	8	204	3178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3033
X-RAY DIFFRACTION	f_angle_d	0.867	4114
X-RAY DIFFRACTION	f_dihedral_angle_d	15.024	1139
X-RAY DIFFRACTION	f_chiral_restr	0.055	480
X-RAY DIFFRACTION	f_plane_restr	0.005	531

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 (%)
1.8-1.85	0.3265	133	0.2784	2661	X-RAY DIFFRACTION	100
1.85-1.91	0.3182	165	0.2342	2622	X-RAY DIFFRACTION	100
1.91-1.98	0.2562	135	0.2253	2676	X-RAY DIFFRACTION	100
1.98-2.06	0.2212	145	0.2125	2657	X-RAY DIFFRACTION	100
2.06-2.15	0.2827	132	0.2046	2673	X-RAY DIFFRACTION	100
2.15-2.27	0.2572	127	0.2065	2680	X-RAY DIFFRACTION	100
2.27-2.41	0.252	108	0.2034	2723	X-RAY DIFFRACTION	100
2.41-2.6	0.2594	138	0.2132	2689	X-RAY DIFFRACTION	100
2.6-2.86	0.265	125	0.2113	2715	X-RAY DIFFRACTION	100
2.86-3.27	0.2343	118	0.207	2737	X-RAY DIFFRACTION	100
3.27-4.12	0.2148	160	0.1739	2714	X-RAY DIFFRACTION	100
4.12-26.53	0.2087	135	0.1884	2853	X-RAY DIFFRACTION	100

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	5.1676	-2.7876	5.0153	5.0173	-2.9423	5.0214	-0.1472	-1.119	0.4922	0.7483	0.0445	0.1568	-0.7404	-0.9088	0.1847	0.4471	0.0545	0.0802	0.4066	-0.0856	0.3184	-0.8654	22.925	10.7696
2	4.9581	-6.3137	0.9736	8.3042	-1.4005	3.8247	0.0551	0.2556	0.0926	-0.2215	-0.2589	-0.1625	0.1268	0.3652	0.1876	0.1674	0.002	0.0108	0.1774	-0.015	0.2655	8.3388	18.2073	-7.5955
3	6.1909	-4.4963	0.11	4.6807	0.0426	0.6024	-0.2355	0.1026	0.0932	-0.1307	-0.1305	-0.3902	0.2982	0.4229	0.1356	0.2591	0.1161	0.0912	0.2945	0.0582	0.252	10.9104	13.8702	-9.1497
4	3.7844	-0.9468	-1.3159	5.8119	-0.0953	3.2543	0.1309	0.0698	0.0685	-0.1357	0.051	0.3703	0.3844	0.0237	-0.1549	0.2047	0.0286	-0.0654	0.1723	0.0263	0.2259	-2.6821	11.0831	-9.7217
5	6.5221	3.3208	-2.9942	6.4444	-5.0029	7.9957	-0.1082	0.4829	-0.0239	-1.0494	0.35	-0.0953	1.2629	0.698	-0.0613	0.5157	0.001	-0.0946	0.2247	-0.0317	0.1857	-1.7454	1.9199	-14.2085
6	5.8018	4.0109	5.5105	6.7673	1.828	7.1367	-0.0143	-0.2713	0.0907	0.1069	-0.0376	0.2626	0.2571	-0.0904	0.0256	0.2601	0.033	0.0388	0.2664	-0.0206	0.1583	0.6868	11.7198	8.4035
7	4.7386	0.0182	0.1858	6.8632	-4.6713	3.5603	-0.0234	-0.6779	-0.0558	-0.1832	-0.5386	-0.7767	0.2382	0.4008	0.5446	0.3307	0.0204	0.0505	0.411	-0.0134	0.2973	10.6134	14.4015	8.3945
8	4.2869	-3.6654	-2.4219	3.7796	1.0979	6.8541	0.0228	-0.2798	0.2137	0.0239	0.0824	-0.5801	-0.0101	0.4209	0.0067	0.3301	0.0038	0.0676	0.3193	-0.0452	0.2777	9.9071	19.9737	1.7599
9	4.6207	-2.4586	3.0498	2.8284	-0.9533	3.7241	-0.1949	-0.2613	0.5415	0.1694	0.0265	-0.0452	-0.0562	0.1446	0.1743	0.3241	0.0069	0.06	0.2268	-0.006	0.2994	2.8427	22.1598	-5.3405
10	1.6419	1.5121	-0.7196	3.1467	0.4042	1.0999	0.3555	0.7483	0.8019	-1.0293	0.2457	1.2404	0.7176	-0.7733	0.6333	0.6051	-0.1087	-0.3305	0.2871	-0.0305	-0.139	-9.0166	4.2689	-14.2894
11	1.3902	0.3181	-0.3197	2.57	0.1798	1.4218	0.0221	0.0714	-0.1354	0.071	0.0007	0.2691	0.0549	0.0822	-0.015	0.131	0.0441	0.0089	0.2139	0.0055	0.2463	28.5751	-1.8648	-18.3658
12	5.0002	1.7807	1.08	5.416	2.8195	7.7213	-0.0074	-0.0318	0.0455	-0.2851	-0.0237	0.4018	0.2038	-0.0668	-0.0046	0.2324	0.0154	-0.029	0.2678	0.0164	0.2809	29.746	-0.8748	-33.0118
13	5.3684	2.7479	-5.4508	1.6455	-2.0966	8.4827	-0.3429	-0.35	-0.8353	-0.6789	-0.1743	0.4052	0.3204	0.3858	0.4029	0.4345	-0.0169	-0.1933	0.3148	-0.0637	0.6288	26.6671	-10.5843	-32.6493
14	1.2677	-1.2705	0.0213	3.4321	-0.2151	1.7867	0.0568	-0.0516	-0.1983	-0.0276	-0.0404	0.6851	0.0118	-0.0967	-0.0025	0.1934	0.0461	0.0263	0.2881	0.0382	0.2508	26.9953	-0.743	-18.3351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 93 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 94 through 103 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 104 through 133 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 134 through 154 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 155 through 171 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 172 through 188 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 189 through 208 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 103 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 104 through 133 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 134 through 154 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 155 through 208 )

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