PDB-8s2f: Crystal structure of Borrelia burgdorferi paralogous family 12 ou...

ID or keywords:

Entry

Database: PDB / ID: 8s2f

Title

Crystal structure of Borrelia burgdorferi paralogous family 12 outer surface protein BBH37

Components

Lipoprotein, putative

Keywords

DNA BINDING PROTEIN / paralogous protein / PFam12

Function / homology

Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein, putative

Function and homology information

Biological species

Borreliella burgdorferi B31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Brangulis, K.

Funding support

Latvia, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Borrelia burgdorferi outer surface protein BBH37
Authors: Brangulis, K.

History

Deposition	Feb 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s2f.cif.gz	85.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2f.ent.gz		Display	PDB format
PDBx/mmJSON format	8s2f.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/s2/8s2f ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2f	HTTPS FTP

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Related structure data

Related structure data	8s2pC C: citing same article (ref.)
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: Lipoprotein, putative

BBB: Lipoprotein, putative

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	37.710, 90.920, 115.250
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lipoprotein, putative Mass: 21136.131 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first 4 residues (GAMG) are remnants from the expression tag. Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_H37 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50692
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.35 Å³/Da / Density % sol: 47.59 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate pH 5.6 20% PEG 4000 20% 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.7→90.92 Å / Num. obs: 11500 / % possible obs: 100 % / Redundancy: 12.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.132 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.7→2.83 Å / Redundancy: 12.9 % / R_merge(I) obs: 0.545 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1471 / CC_1/2: 0.962 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→71.382 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.86 / Cross valid method: FREE R-VALUE / ESU R Free: 0.442
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3099	596	5.205 %
R_work	0.2213	10854	-
all	0.226	-	-
obs	-	11450	99.948 %

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: 45.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.017 Å²	0 Å²	0 Å²
2-	-	0.009 Å²	-0 Å²
3-	-	-	-0.026 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→71.382 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2888	0	0	29	2917

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2916
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.016	2905
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.639	3888
X-RAY DIFFRACTION	r_angle_other_deg	2.264	1.596	6718
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.872	5	359
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.619	23.636	165
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.65	15	619
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.429	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	388
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3274
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	642
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	722
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.228	0.2	2633
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1411
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	1591
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.147	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.275	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	3.186	4.483	1442
X-RAY DIFFRACTION	r_mcbond_other	3.174	4.481	1441
X-RAY DIFFRACTION	r_mcangle_it	5.059	6.721	1799
X-RAY DIFFRACTION	r_mcangle_other	5.06	6.723	1800
X-RAY DIFFRACTION	r_scbond_it	3.902	5.115	1474
X-RAY DIFFRACTION	r_scbond_other	3.901	5.115	1474
X-RAY DIFFRACTION	r_scangle_it	6.504	7.431	2089
X-RAY DIFFRACTION	r_scangle_other	6.503	7.433	2090
X-RAY DIFFRACTION	r_lrange_it	9.029	53.851	3297
X-RAY DIFFRACTION	r_lrange_other	9.029	53.879	3297

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.7-2.77	0.414	38	0.297	764	0.303	802	0.764	0.792	100	0.272
2.77-2.846	0.415	51	0.292	764	0.3	815	0.785	0.822	100	0.262
2.846-2.928	0.373	34	0.266	748	0.27	782	0.736	0.862	100	0.241
2.928-3.018	0.363	43	0.252	718	0.258	761	0.826	0.862	100	0.225
3.018-3.117	0.366	51	0.221	704	0.229	755	0.815	0.902	100	0.205
3.117-3.226	0.308	39	0.22	667	0.225	707	0.883	0.91	99.8586	0.208
3.226-3.348	0.335	38	0.221	649	0.227	687	0.867	0.91	100	0.206
3.348-3.484	0.341	23	0.204	659	0.208	682	0.865	0.922	100	0.194
3.484-3.639	0.237	31	0.223	613	0.223	645	0.912	0.906	99.845	0.214
3.639-3.816	0.335	28	0.242	602	0.247	631	0.866	0.891	99.8415	0.225
3.816-4.021	0.323	27	0.227	542	0.232	569	0.875	0.9	100	0.22
4.021-4.265	0.263	31	0.211	542	0.214	573	0.904	0.913	100	0.202
4.265-4.558	0.285	32	0.186	500	0.193	532	0.899	0.936	100	0.186
4.558-4.921	0.202	26	0.191	467	0.192	493	0.936	0.939	100	0.188
4.921-5.388	0.272	20	0.202	452	0.205	472	0.894	0.935	100	0.2
5.388-6.02	0.46	25	0.254	388	0.265	413	0.861	0.895	100	0.244
6.02-6.943	0.353	25	0.28	352	0.286	378	0.89	0.891	99.7355	0.278
6.943-8.484	0.283	18	0.206	307	0.211	325	0.932	0.943	100	0.217
8.484-11.914	0.193	10	0.138	257	0.14	267	0.949	0.974	100	0.162
11.914-71.382	0.263	6	0.222	158	0.224	166	0.974	0.949	98.7952	0.29

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