PDB-2ga0: Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)

ID or keywords:

Entry

Database: PDB / ID: 2ga0

Title

Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)

Components

surface protein VspA

Keywords

IMMUNE SYSTEM /

helical bundle / Ni(II) binding sites

Function / homology

Function and homology information

cell outer membrane
Similarity search - Function

Biological species

Borrelia turicatae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Lawson, C.L. / Yung, B.H. / Barbour, A.G. / Zuckert, W.R.

Citation

Journal: J.Bacteriol. / Year: 2006
Title: Crystal structure of neurotropism-associated variable surface protein 1 (Vsp1) of Borrelia turicatae.
Authors: Lawson, C.L. / Yung, B.H. / Barbour, A.G. / Zuckert, W.R.

History

Deposition	Mar 7, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ga0.cif.gz	236 KB	Display	PDBx/mmCIF format
PDB format	pdb2ga0.ent.gz	191.7 KB	Display	PDB format
PDBx/mmJSON format	2ga0.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/ga/2ga0 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/2ga0	HTTPS FTP

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Related structure data

Related structure data	1yjgSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ggq-1 3iee-d 2w2b-d 1p69-d 4lmo-1 5c4v-2 6e31-d 5v0r-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1yjgSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

A: surface protein VspA

B: surface protein VspA

C: surface protein VspA

D: surface protein VspA

E: surface protein VspA

F: surface protein VspA

G: surface protein VspA

H: surface protein VspA

hetero molecules

149 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: surface protein VspA

B: surface protein VspA

hetero molecules

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

2

C: surface protein VspA

D: surface protein VspA

hetero molecules

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

3

E: surface protein VspA

F: surface protein VspA

hetero molecules

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

4

G: surface protein VspA

H: surface protein VspA

hetero molecules

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

Unit cell

Length a, b, c (Å)	241.835, 69.105, 87.578
Angle α, β, γ (deg.)	90.00, 104.95, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	LEU	LEU	A	A	41 - 201	8 - 168
2	1	LEU	LEU	LEU	LEU	B	B	41 - 201	8 - 168
3	1	LEU	LEU	LEU	LEU	C	C	41 - 201	8 - 168
4	1	LEU	LEU	LEU	LEU	D	D	41 - 201	8 - 168
5	1	LEU	LEU	LEU	LEU	E	E	41 - 201	8 - 168
6	1	LEU	LEU	LEU	LEU	F	F	41 - 201	8 - 168
7	1	LEU	LEU	LEU	LEU	G	G	41 - 201	8 - 168
8	1	LEU	LEU	LEU	LEU	H	H	41 - 201	8 - 168
1	2	VAL	VAL	THR	THR	A	A	38 - 43	5 - 10
2	2	VAL	VAL	THR	THR	C	C	38 - 43	5 - 10
3	2	VAL	VAL	THR	THR	E	E	38 - 43	5 - 10
4	2	VAL	VAL	THR	THR	G	G	38 - 43	5 - 10
1	3	VAL	VAL	THR	THR	B	B	38 - 43	5 - 10
2	3	VAL	VAL	THR	THR	D	D	38 - 43	5 - 10
3	3	VAL	VAL	THR	THR	F	F	38 - 43	5 - 10
4	3	VAL	VAL	THR	THR	H	H	38 - 43	5 - 10

NCS ensembles :

ID
1
2
3

#1: Protein	surface protein VspA / / Variable Surface Protein 1 Mass: 18500.959 Da / Num. of mol.: 8 / Fragment: residues 34-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia turicatae (bacteria) / Gene: Vsp1, VspA / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34000
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O

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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: 48.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28% (w/v) polyethylene glycol (PEG), 80 mM Tris HCl, 15% (v/v) glycerol, 100 mM NiCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 2000
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. all: 38032 / Num. obs: 38032 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_merge(I) obs: 0.042 / Χ²: 0.472 / Net I/σ(I): 12.5
Reflection shell	Resolution: 2.7→2.8 Å / % possible obs: 92 % / R_merge(I) obs: 0.147 / Num. unique obs: 3523 / Χ²: 0.279 / % possible all: 92

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YJG

1yjg

Resolution: 2.7→50 Å / Cor.coef. F_o:F_c: 0.924 / Cor.coef. F_o:F_c free: 0.876 / SU B: 14.486 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.272	1902	5 %	RANDOM
R_work	0.216	-	-	-
all	0.219	38031	-	-
obs	0.219	38031	98.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.313 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.04 Å²	0 Å²	-0.92 Å²
2-	-	1.91 Å²	0 Å²
3-	-	-	-1.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9456	0	14	136	9606

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	9502
X-RAY DIFFRACTION	r_angle_refined_deg	1.544	1.985	12784
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.121	5	1304
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1696
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6400
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	5372
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.173	0.2	366
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.245	0.2	84
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.383	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.263	1.5	6480
X-RAY DIFFRACTION	r_mcangle_it	0.589	2	10360
X-RAY DIFFRACTION	r_scbond_it	2.429	3	3022
X-RAY DIFFRACTION	r_scangle_it	2.486	4.5	2424

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	644	TIGHT POSITIONAL	0.07	0.05
1	2	B	644	TIGHT POSITIONAL	0.06	0.05
1	3	C	644	TIGHT POSITIONAL	0.06	0.05
1	4	D	644	TIGHT POSITIONAL	0.06	0.05
1	5	E	644	TIGHT POSITIONAL	0.07	0.05
1	6	F	644	TIGHT POSITIONAL	0.07	0.05
1	7	G	644	TIGHT POSITIONAL	0.07	0.05
1	8	H	644	TIGHT POSITIONAL	0.06	0.05
1	1	A	515	MEDIUM POSITIONAL	0.51	0.5
1	2	B	515	MEDIUM POSITIONAL	0.64	0.5
1	3	C	515	MEDIUM POSITIONAL	0.55	0.5
1	4	D	515	MEDIUM POSITIONAL	0.53	0.5
1	5	E	515	MEDIUM POSITIONAL	0.53	0.5
1	6	F	515	MEDIUM POSITIONAL	0.61	0.5
1	7	G	515	MEDIUM POSITIONAL	0.61	0.5
1	8	H	515	MEDIUM POSITIONAL	0.59	0.5
1	1	A	644	TIGHT THERMAL	0.11	0.5
1	2	B	644	TIGHT THERMAL	0.1	0.5
1	3	C	644	TIGHT THERMAL	0.1	0.5
1	4	D	644	TIGHT THERMAL	0.1	0.5
1	5	E	644	TIGHT THERMAL	0.1	0.5
1	6	F	644	TIGHT THERMAL	0.1	0.5
1	7	G	644	TIGHT THERMAL	0.1	0.5
1	8	H	644	TIGHT THERMAL	0.09	0.5
1	1	A	515	MEDIUM THERMAL	1.05	2
1	2	B	515	MEDIUM THERMAL	0.84	2
1	3	C	515	MEDIUM THERMAL	0.81	2
1	4	D	515	MEDIUM THERMAL	0.93	2
1	5	E	515	MEDIUM THERMAL	0.86	2
1	6	F	515	MEDIUM THERMAL	0.84	2
1	7	G	515	MEDIUM THERMAL	0.83	2
1	8	H	515	MEDIUM THERMAL	0.72	2
2	1	A	24	TIGHT POSITIONAL	0.04	0.05
2	2	C	24	TIGHT POSITIONAL	0.04	0.05
2	3	E	24	TIGHT POSITIONAL	0.04	0.05
2	4	G	24	TIGHT POSITIONAL	0.04	0.05
2	1	A	19	MEDIUM POSITIONAL	0.62	0.5
2	2	C	19	MEDIUM POSITIONAL	0.4	0.5
2	3	E	19	MEDIUM POSITIONAL	0.49	0.5
2	4	G	19	MEDIUM POSITIONAL	0.49	0.5
2	1	A	24	TIGHT THERMAL	0.05	0.5
2	2	C	24	TIGHT THERMAL	0.05	0.5
2	3	E	24	TIGHT THERMAL	0.05	0.5
2	4	G	24	TIGHT THERMAL	0.05	0.5
2	1	A	19	MEDIUM THERMAL	0.45	2
2	2	C	19	MEDIUM THERMAL	0.52	2
2	3	E	19	MEDIUM THERMAL	0.39	2
2	4	G	19	MEDIUM THERMAL	0.48	2
3	1	B	24	TIGHT POSITIONAL	0.04	0.05
3	2	D	24	TIGHT POSITIONAL	0.06	0.05
3	3	F	24	TIGHT POSITIONAL	0.04	0.05
3	4	H	24	TIGHT POSITIONAL	0.04	0.05
3	1	B	19	MEDIUM POSITIONAL	0.6	0.5
3	2	D	19	MEDIUM POSITIONAL	0.67	0.5
3	3	F	19	MEDIUM POSITIONAL	0.44	0.5
3	4	H	19	MEDIUM POSITIONAL	0.53	0.5
3	1	B	24	TIGHT THERMAL	0.05	0.5
3	2	D	24	TIGHT THERMAL	0.06	0.5
3	3	F	24	TIGHT THERMAL	0.04	0.5
3	4	H	24	TIGHT THERMAL	0.04	0.5
3	1	B	19	MEDIUM THERMAL	0.55	2
3	2	D	19	MEDIUM THERMAL	0.47	2
3	3	F	19	MEDIUM THERMAL	0.3	2
3	4	H	19	MEDIUM THERMAL	0.28	2

LS refinement shell

Resolution: 2.705→2.775 Å / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.353	119
R_work	0.286	2418
obs	-	2537

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	4.7673	-1.5431	-1.0291	2.1532	1.0053	2.5722	-0.0122	-0.0933	-0.2613	0.1019	0.0173	0.2995	-0.1418	-0.2179	-0.005	0.0655	0.0226	0.0038	0.105	-0.0223	0.0781	-32.18	-36.6191	15.7153
2	3.3719	-1.0405	-0.8896	2.8619	0.2388	2.2592	0.2832	0.5565	0.3159	-0.3487	-0.2454	-0.0283	-0.4154	-0.2781	-0.0379	0.1184	0.1262	0.0129	0.2459	-0.0115	0.1237	-25.3213	-30.0902	1.889
3	5.3765	0.1881	-0.1048	3.9931	0.802	3.1211	0.0037	-0.3351	-0.5127	0.2539	0.0137	0.0506	0.7174	0.0721	-0.0174	0.2889	0.0199	0.034	0.0607	0.0068	0.1556	-31.3201	-70.8433	14.0947
4	4.2393	-0.0581	-0.3978	5.0192	0.3243	2.6802	-0.3409	0.4223	-0.2542	-0.3558	0.4547	-0.2997	0.3372	0.1853	-0.1138	0.1063	0.0057	0.0381	0.1675	-0.1206	0.1299	-23.3445	-63.6791	1.25
5	3.6532	-0.2361	1.6628	1.9721	0.261	4.7117	-0.1335	0.2543	0.3511	-0.0858	0.0089	0.0442	-0.8474	-0.1605	0.1245	0.3504	0.1751	0.0368	0.0963	0.0187	0.1231	-15.7687	-23.8539	-40.3894
6	3.1516	0.4177	0.9865	3.1386	-0.0006	4.0324	0.0313	-0.2615	0.1281	0.2127	-0.0044	0.1196	-0.5357	-0.5313	-0.0268	0.1691	0.1388	0.0045	0.1734	-0.0507	0.0499	-15.3944	-30.8063	-25.194
7	4.2216	3.3461	3.0535	5.7447	3.9604	4.9376	-0.0373	0.1361	-0.1474	-0.4058	0.0506	-0.17	-0.042	-0.0792	-0.0133	0.1515	-0.0214	0.0699	0.126	-0.0347	0.165	-39.1189	-58.0306	42.3827
8	3.2323	2.833	1.2944	5.8519	2.0371	3.4945	0.789	-0.4532	-0.6162	1.0068	-0.5615	-0.4268	0.7819	-0.69	-0.2275	0.3809	-0.2441	-0.113	0.3441	0.0458	0.2482	-40.5997	-64.322	57.8956

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 38 - 201 / Label seq-ID: 5 - 168

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B
3	3	C	C
4	4	D	D
5	5	E	E
6	6	F	F
7	7	G	G
8	8	H	H

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