PDB-8q4k: Crystal structure of Borrelia burgdorferi BB0158

ID or keywords:

Entry

Database: PDB / ID: 8q4k

Title

Crystal structure of Borrelia burgdorferi BB0158

Components

S2 lipoprotein

Keywords

MEMBRANE PROTEIN / Lyme disease / outer surface protein / borreliosis.

Function / homology

Prokaryotic membrane lipoprotein lipid attachment site profile. / S2 lipoprotein

Function and homology information

Biological species

Borreliella burgdorferi B31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Brangulis, K. / Tars, K.

Funding support

European Union, 1items

Citation

Journal: Ticks Tick Borne Dis / Year: 2024
Title: Structural studies of chromosomally encoded outer surface lipoprotein BB0158 from Borrelia burgdorferi sensu stricto.
Authors: Brangulis, K. / Akopjana, I. / Bogans, J. / Kazaks, A. / Tars, K.

History

Deposition	Aug 7, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q4k.cif.gz	175.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8q4k.ent.gz		Display	PDB format
PDBx/mmJSON format	8q4k.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/q4/8q4k ftp://data.pdbj.org/pub/pdb/validation_reports/q4/8q4k	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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

AAA: S2 lipoprotein

BBB: S2 lipoprotein

CCC: S2 lipoprotein

DDD: S2 lipoprotein

hetero molecules

97.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: S2 lipoprotein

BBB: S2 lipoprotein

hetero molecules

defined by author
Evidence: gel filtration
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: S2 lipoprotein

DDD: S2 lipoprotein

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.063, 81.774, 80.801
Angle α, β, γ (deg.)	90.000, 109.381, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	S2 lipoprotein Mass: 24208.658 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51180
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.42 Å³/Da / Density % sol: 49.28 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M ammonium sulfate 0.1 M sodium acetate (pH 4.6) 20% PEG 2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.4→44.97 Å / Num. obs: 35959 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.074 / Net I/σ(I): 15
Reflection shell	Resolution: 2.4→2.49 Å / R_merge(I) obs: 0.403 / Mean I/σ(I) obs: 4 / Num. unique obs: 3725 / CC_1/2: 0.938

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→44.97 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.885 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.323
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2973	1821	5.066 %
R_work	0.213	34128	-
all	0.217	-	-
obs	-	35949	99.255 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.838 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.002 Å²	0 Å²	0.004 Å²
2-	-	-0.003 Å²	-0 Å²
3-	-	-	0.002 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→44.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6473	0	15	248	6736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	6603
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.016	6434
X-RAY DIFFRACTION	r_angle_refined_deg	1.567	1.637	8897
X-RAY DIFFRACTION	r_angle_other_deg	2.287	1.586	14959
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.818	5	802
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.938	26.545	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.399	15	1301
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	894
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7196
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1308
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1220
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.222	0.2	5933
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	3076
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	2895
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	287
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.064	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.343	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.303	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.103	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	4.115	4.979	3223
X-RAY DIFFRACTION	r_mcbond_other	4.113	4.979	3222
X-RAY DIFFRACTION	r_mcangle_it	6.044	7.45	4020
X-RAY DIFFRACTION	r_mcangle_other	6.044	7.45	4021
X-RAY DIFFRACTION	r_scbond_it	4.24	5.371	3380
X-RAY DIFFRACTION	r_scbond_other	4.206	5.363	3369
X-RAY DIFFRACTION	r_scangle_it	6.417	7.878	4877
X-RAY DIFFRACTION	r_scangle_other	6.417	7.866	4860
X-RAY DIFFRACTION	r_lrange_it	9.115	57.489	7112
X-RAY DIFFRACTION	r_lrange_other	9.109	57.47	7099

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 (%)
2.4-2.462	0.359	143	0.275	2511	X-RAY DIFFRACTION	99.6246
2.462-2.53	0.346	133	0.27	2415	X-RAY DIFFRACTION	98.2267
2.53-2.603	0.295	121	0.232	2402	X-RAY DIFFRACTION	99.3698
2.603-2.683	0.36	137	0.262	2284	X-RAY DIFFRACTION	99.5068
2.683-2.771	0.395	111	0.268	2253	X-RAY DIFFRACTION	99.5788
2.771-2.868	0.376	101	0.23	2193	X-RAY DIFFRACTION	99.2644
2.868-2.976	0.327	105	0.212	2086	X-RAY DIFFRACTION	99.6362
2.976-3.097	0.317	104	0.22	2039	X-RAY DIFFRACTION	99.6744
3.097-3.235	0.316	107	0.224	1904	X-RAY DIFFRACTION	98.0976
3.235-3.392	0.318	111	0.228	1843	X-RAY DIFFRACTION	99.4402
3.392-3.576	0.319	109	0.237	1771	X-RAY DIFFRACTION	99.8407
3.576-3.792	0.271	81	0.214	1667	X-RAY DIFFRACTION	99.6011
3.792-4.053	0.244	90	0.179	1583	X-RAY DIFFRACTION	99.7615
4.053-4.377	0.223	73	0.165	1458	X-RAY DIFFRACTION	99.5449
4.377-4.793	0.241	67	0.164	1344	X-RAY DIFFRACTION	97.6471
4.793-5.356	0.271	64	0.178	1236	X-RAY DIFFRACTION	99.3884
5.356-6.18	0.325	67	0.215	1067	X-RAY DIFFRACTION	99.561
6.18-7.556	0.333	35	0.239	949	X-RAY DIFFRACTION	99.2936
7.556-10.634	0.283	33	0.179	712	X-RAY DIFFRACTION	98.545
10.634-44.97	0.258	29	0.254	411	X-RAY DIFFRACTION	98.2143

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