PDB-9azz: Crystal structure of outer membrane lipoprotein carrier protein (...

ID or keywords:

Entry

Database: PDB / ID: 9azz

Title

Crystal structure of outer membrane lipoprotein carrier protein (LolA) from Ehrlichia ruminantium

Components

Outer membrane lipoprotein carrier protein LolA

Keywords

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

Function / homology

Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA

Function and homology information

Biological species

Ehrlichia ruminantium str. Gardel (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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 Ehrlichia ruminantium
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Mar 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9azz.cif.gz	223.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9azz.ent.gz	179.7 KB	Display	PDB format
PDBx/mmJSON format	9azz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9azz_validation.pdf.gz	643.8 KB	Display	wwPDB validaton report
Full document	9azz_full_validation.pdf.gz	649.1 KB	Display
Data in XML	9azz_validation.xml.gz	21.4 KB	Display
Data in CIF	9azz_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/9azz ftp://data.pdbj.org/pub/pdb/validation_reports/az/9azz	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

Deposited unit

A: Outer membrane lipoprotein carrier protein LolA

B: Outer membrane lipoprotein carrier protein LolA

C: Outer membrane lipoprotein carrier protein LolA

hetero molecules

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

1

A: Outer membrane lipoprotein carrier protein LolA

hetero molecules

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

2

B: Outer membrane lipoprotein carrier protein LolA

hetero molecules

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

3

C: Outer membrane lipoprotein carrier protein LolA

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

Unit cell

Length a, b, c (Å)	80.647, 53.021, 80.802
Angle α, β, γ (deg.)	90.00, 116.96, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Outer membrane lipoprotein carrier protein LolA Mass: 21515.209 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ehrlichia ruminantium str. Gardel (bacteria) Gene: EDL81_04530 / Plasmid: EhruA.17554.a.VH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6I6ARN1
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: JCSG+ A8: 0.2M Ammonium Formate, pH 4.6, 20% PEG 3350, EhruA.17554.a.VH2.PW39214 at 22.3 mg/mL. AC Plate 21 LolA A10. Puck: PSL-2103, Cryo: 80% crystallant + 20% glycerol. Density consistent ...Details: JCSG+ A8: 0.2M Ammonium Formate, pH 4.6, 20% PEG 3350, EhruA.17554.a.VH2.PW39214 at 22.3 mg/mL. AC Plate 21 LolA A10. Puck: PSL-2103, Cryo: 80% crystallant + 20% glycerol. Density consistent with a PEG fragment observed in subunit B

Crystal

Density Matthews: 2.39 Å³/Da / Density % sol: 48.44 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JCSG+ A8: 0.2M Ammonium Formate, pH 4.6, 20% PEG 3350, EhruA.17554.a.VH2.PW39214 at 22.3 mg/mL. AC Plate 21 LolA A10. Puck: PSL-2103, Cryo: 80% crystallant + 20% glycerol. Density consistent ...

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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: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 3, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2→42.7 Å / Num. obs: 41393 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.99 / R_merge(I) obs: 0.163 / R_pim(I) all: 0.069 / R_rim(I) all: 0.178 / Χ²: 1.03 / Net I/σ(I): 6.5 / Num. measured all: 279537
Reflection shell	Resolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 7 % / R_merge(I) obs: 1.293 / Num. measured all: 21518 / Num. unique obs: 3080 / CC_1/2: 0.718 / R_pim(I) all: 0.525 / R_rim(I) all: 1.397 / Χ²: 0.99 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5250: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→42.7 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2618	1980	4.79 %
R_work	0.216	-	-
obs	0.2182	41335	99.72 %

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→42.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4089	0	25	117	4231

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4223
X-RAY DIFFRACTION	f_angle_d	1.076	5752
X-RAY DIFFRACTION	f_dihedral_angle_d	13.238	1556
X-RAY DIFFRACTION	f_chiral_restr	0.067	670
X-RAY DIFFRACTION	f_plane_restr	0.01	729

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 (%)
2-2.05	0.2845	134	0.264	2822	X-RAY DIFFRACTION	100
2.05-2.11	0.3024	129	0.2656	2775	X-RAY DIFFRACTION	100
2.11-2.17	0.3094	128	0.2643	2783	X-RAY DIFFRACTION	100
2.17-2.24	0.2674	130	0.2558	2831	X-RAY DIFFRACTION	100
2.24-2.32	0.279	131	0.2427	2795	X-RAY DIFFRACTION	100
2.32-2.41	0.3122	138	0.2447	2813	X-RAY DIFFRACTION	100
2.41-2.52	0.2579	130	0.2445	2808	X-RAY DIFFRACTION	100
2.52-2.65	0.305	165	0.2466	2766	X-RAY DIFFRACTION	100
2.65-2.82	0.3476	172	0.2581	2776	X-RAY DIFFRACTION	100
2.82-3.04	0.2882	153	0.2438	2805	X-RAY DIFFRACTION	100
3.04-3.34	0.2562	168	0.2191	2817	X-RAY DIFFRACTION	100
3.34-3.82	0.252	138	0.2074	2816	X-RAY DIFFRACTION	100
3.83-4.82	0.2168	119	0.1711	2848	X-RAY DIFFRACTION	99
4.82-42.7	0.2371	145	0.1999	2900	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	3.0737	-0.8566	2.6562	9.1248	-4.163	3.6784	-0.2685	-0.1928	-0.1243	0.2658	-0.1647	-1.0194	0.1686	0.5825	0.4819	0.3393	0.0055	-0.0235	0.397	0.0656	0.3224	41.1887	21.0283	29.725
2	8.7617	6.4914	-2.1163	7.3488	-0.3968	2.7268	0.0011	0.0604	-0.702	-0.1559	-0.0165	-0.4122	-0.2329	0.0514	0.0005	0.2213	0.0441	-0.0287	0.291	-0.0147	0.219	23.5483	24.52	19.3814
3	7.67	4.1611	0.8623	6.4335	0.3514	2.3335	-0.1929	0.2039	-0.0478	-0.2513	0.1432	0.3631	-0.1076	-0.0847	-0.0156	0.3105	0.0553	0.0113	0.3351	-0.0139	0.2258	15.7062	22.2209	22.3379
4	3.5944	4.3018	2.4016	5.6106	2.5372	2.7405	-0.1019	-0.0964	0.865	0.059	-0.0174	0.6157	-0.1059	-0.0941	0.1346	0.3353	0.0044	-0.0272	0.2601	-0.0749	0.2977	17.0593	30.9228	22.6377
5	3.0239	2.19	4.2948	5.643	0.7238	9.54	0.1361	-0.9774	-0.0122	0.2415	-0.2289	0.8893	0.5159	-1.0992	0.1089	0.3498	0.033	-0.0399	0.4204	-0.144	0.4496	10.8233	36.0078	28.0958
6	6.1386	-3.3652	0.5	5.795	-1.7045	3.8673	0.0868	-0.1195	0.0046	0.5412	-0.3379	0.0174	0.2592	0.1309	0.2585	0.3791	-0.0807	-0.0245	0.4155	0.0586	0.436	31.8228	23.4313	32.0448
7	6.528	-1.6503	-2.1922	5.3167	0.822	5.7534	-0.2198	-0.4129	-0.8056	0.6169	-0.048	-0.1189	1.159	-0.5346	0.0868	0.4301	-0.0221	-0.09	0.3721	0.0917	0.3361	29.2567	17.626	32.3087
8	3.6736	0.0266	0.6059	4.935	-3.8724	6.749	0.016	-0.2729	-0.3189	0.0701	0.16	0.145	0.0731	-0.4229	-0.1543	0.242	-0.0051	-0.0332	0.2359	-0.0263	0.2849	24.2794	17.7645	24.9763
9	5.3128	1.8991	-1.51	7.9564	3.4096	3.8411	-0.2462	0.4721	0.3054	-1.5664	0.1266	0.0179	-0.3282	0.4114	0.1909	0.4135	0.0399	0.0017	0.3798	0.0719	0.2411	27.2095	32.7195	13.9277
10	9.0734	2.2949	6.4456	0.8378	0.537	8.7621	-0.554	-0.4428	1.1064	-0.7962	-0.0272	1.642	-1.8745	-1.3351	0.5004	0.7169	0.103	-0.3401	0.7016	-0.0134	0.9099	8.6243	41.2797	15.3282
11	3.9296	1.4476	0.7932	8.239	2.7073	2.7999	0.2838	-1.7105	-0.5525	1.0606	-0.2835	0.5714	0.4023	0.2935	-0.0145	0.4932	0.0517	0.1519	0.4413	0.086	0.4453	-20.9546	4.3723	57.1131
12	6.5549	-2.0438	-2.2671	6.842	3.117	8.6901	-0.1388	-0.023	0.1686	-0.6843	0.1713	-0.2445	-0.4555	0.0698	-0.0203	0.1473	0.0381	-0.0179	0.1625	0.043	0.1807	-3.6561	7.1871	39.6116
13	4.8956	-0.9264	-2.4517	3.4225	-1.6721	6.9928	0.1753	0.5692	0.5475	-0.2424	0.0653	-0.2711	-0.4258	-0.5517	-0.2346	0.2516	0.0089	-0.0083	0.2431	0.0419	0.341	-4.2849	16.4417	33.8663
14	0.5575	-1.3304	1.8741	8.2262	-5.1328	6.3994	0.2948	0.6644	1.3806	0.0132	0.4034	0.3566	-0.1726	-0.9245	-0.911	0.4006	0.236	0.0498	0.5117	0.207	0.6063	-12.5429	20.1506	30.8592
15	5.8824	-0.3592	0.6604	2.145	-0.326	4.33	-0.0996	0.0347	-0.211	-0.025	-0.03	0.2496	-0.0564	-0.1991	0.1734	0.4419	0.015	0.1379	0.3225	-0.0178	0.3727	-19.535	7.9392	48.4922
16	8.4195	-1.7903	5.3865	6.973	-1.9439	6.549	0.0407	0.2865	-1.0487	-0.1569	0.1546	0.2832	0.4506	0.072	-0.2155	0.346	0.0121	0.1384	0.373	-0.0802	0.3573	-16.6117	0.5324	46.8179
17	7.4928	0.9901	2.3431	4.743	2.0258	1.7077	-0.307	-0.0521	0.1002	0.2805	-0.0683	0.0637	-0.1162	-0.2002	0.2872	0.323	-0.0393	0.0801	0.2783	-0.0171	0.2776	-9.3112	1.9187	43.9395
18	4.0034	-2.0832	3.5684	6.0463	-5.0773	8.6724	0.2146	0.1973	0.7374	0.0823	-0.3043	-0.5867	-0.8573	1.1325	0.1795	0.3641	-0.0631	-0.016	0.3673	-0.0977	0.4291	-0.6317	18.308	46.5846
19	1.5475	-1.3638	1.5885	2.4964	-0.5891	6.8597	-0.0004	-0.3571	0.086	0.2023	0.0144	0.0285	-0.2499	-0.5612	-0.047	0.3991	-0.0006	0.0263	0.3183	-0.0099	0.2326	8.4381	21.3494	-7.7125
20	9.272	1.3188	-2.6168	0.1997	-0.3177	0.9641	-1.3082	-0.3194	-0.4917	-0.7423	0.8812	-0.3912	0.6376	-0.3916	0.4609	0.6304	0.0323	0.0599	0.4653	0.0354	0.4452	5.2194	21.654	1.2734
21	4.8897	1.1266	-0.2822	4.3104	-2.1152	5.6565	0.0372	-0.2818	-0.0847	0.2065	0.1133	-0.1421	0.3938	0.0207	-0.1654	0.3937	-0.013	-0.0264	0.3336	-0.0279	0.2005	12.6819	13.8695	-0.0405
22	-0.0368	0.0124	-0.0263	0.6977	-1.9548	5.1629	-0.0407	0.902	0.882	0.2169	0.001	-0.2485	-1.5844	0.6454	-0.0249	0.7392	0.0419	0.0579	0.8429	0.0934	0.3365	10.1966	33.2015	-22.1861

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 45 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 65 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 66 through 83 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 84 through 112 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 113 through 132 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 133 through 155 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 156 through 167 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 168 through 178 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 19 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 20 through 45 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 46 through 77 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 78 through 86 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 87 through 110 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 111 through 132 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 133 through 155 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 156 through 171 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 5 through 83 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 84 through 93 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 94 through 167 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 168 through 178 )

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