PDB-8tv3: Fab 221-5 in complex with OspA

ID or keywords:

Entry

Database: PDB / ID: 8tv3

Title

Fab 221-5 in complex with OspA

Components

Heavy chain of human monoclonal Fab 221-5
Light chain of human monoclonal Fab 22105
Outer surface protein A

Keywords

IMMUNE SYSTEM / human monoclonal antibody / outer surface protein

Function / homology

Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer surface protein A

Function and homology information

Biological species

Homo sapiens (human)

Borreliella burgdorferi B31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.312 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab 221-5 in complex with OspA
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	Aug 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tv3.cif.gz	266.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8tv3.ent.gz	211.8 KB	Display	PDB format
PDBx/mmJSON format	8tv3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tv3_validation.pdf.gz	734.5 KB	Display	wwPDB validaton report
Full document	8tv3_full_validation.pdf.gz	747.7 KB	Display
Data in XML	8tv3_validation.xml.gz	26.7 KB	Display
Data in CIF	8tv3_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/8tv3 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tv3	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
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #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)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#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

L: Light chain of human monoclonal Fab 22105

H: Heavy chain of human monoclonal Fab 221-5

A: Outer surface protein A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	63.819, 90.963, 211.962
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁22₁

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Protein , 1 types, 1 molecules A

#3: Protein	Outer surface protein A Mass: 27595.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: ospA / Production host: Escherichia coli B (bacteria) / References: UniProt: D2Y4L7

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Antibody , 2 types, 2 molecules LH

#1: Antibody	Light chain of human monoclonal Fab 22105 Mass: 23410.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Heavy chain of human monoclonal Fab 221-5 Mass: 24438.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 236 molecules

#4: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 4.14 Å³/Da / Density % sol: 70.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM MES pH 6.5, 30% PEG 600, 5% PEG 1000, and 10% glycerol.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 53784 / % possible obs: 98.4 % / Redundancy: 4.4 % / CC_1/2: 0.63 / Net I/σ(I): 5.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	3.3	0.828	2629	0.631	0.88	0.495	0.97	0.525	96.8
2.34-2.38	3.4	0.813	2596	0.623	0.876	0.483	0.951	0.496	97.7
2.38-2.43	3.5	0.813	2633	0.669	0.895	0.48	0.95	0.524	97.3
2.43-2.48	3.5	0.76	2640	0.735	0.921	0.445	0.886	0.522	98.3
2.48-2.53	3.4	0.722	2543	0.683	0.901	0.423	0.842	0.539	94.5
2.53-2.59	3.6	0.739	2630	0.716	0.913	0.424	0.857	0.554	97.3
2.59-2.66	4.3	0.584	2660	0.867	0.964	0.306	0.662	0.561	98.3
2.66-2.73	4.4	0.534	2664	0.883	0.968	0.273	0.602	0.569	98.8
2.73-2.81	4.5	0.444	2663	0.922	0.979	0.225	0.5	0.608	98.6
2.81-2.9	4.5	0.355	2701	0.951	0.987	0.179	0.399	0.645	98.5
2.9-3	4.6	0.279	2668	0.962	0.99	0.141	0.314	0.667	99.1
3-3.12	4.8	0.238	2683	0.974	0.993	0.119	0.267	0.725	99.4
3.12-3.26	5	0.185	2699	0.983	0.996	0.09	0.207	0.881	99.3
3.26-3.44	5.1	0.144	2726	0.986	0.997	0.07	0.161	1.033	99.8
3.44-3.65	4.7	0.117	2704	0.988	0.997	0.059	0.132	1.33	98.9
3.65-3.93	4.9	0.101	2714	0.99	0.998	0.05	0.113	1.39	98.2
3.93-4.33	5.2	0.079	2734	0.995	0.999	0.038	0.088	1.578	99.4
4.33-4.95	4.9	0.061	2779	0.996	0.999	0.031	0.069	1.605	99.6
4.95-6.24	4.7	0.06	2796	0.995	0.999	0.031	0.068	1.376	99.3
6.24-50	4.4	0.047	2922	0.997	0.999	0.024	0.053	1.438	98

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.312→46.859 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2273	2645	4.93 %
R_work	0.1994	-	-
obs	0.2008	53698	97.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.312→46.859 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4759	0	22	230	5011

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4892
X-RAY DIFFRACTION	f_angle_d	0.765	6615
X-RAY DIFFRACTION	f_dihedral_angle_d	3.38	3689
X-RAY DIFFRACTION	f_chiral_restr	0.051	757
X-RAY DIFFRACTION	f_plane_restr	0.004	833

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 (%)
2.312-2.3544	0.3064	118	0.2882	2373	X-RAY DIFFRACTION	87
2.3544-2.3997	0.3367	137	0.2804	2614	X-RAY DIFFRACTION	98
2.3997-2.4487	0.3094	139	0.2632	2634	X-RAY DIFFRACTION	97
2.4487-2.5019	0.3091	121	0.2603	2647	X-RAY DIFFRACTION	98
2.5019-2.5601	0.2801	125	0.2565	2590	X-RAY DIFFRACTION	94
2.5601-2.6241	0.3166	137	0.2402	2615	X-RAY DIFFRACTION	98
2.6241-2.6951	0.2948	125	0.2252	2707	X-RAY DIFFRACTION	98
2.6951-2.7744	0.266	147	0.2177	2705	X-RAY DIFFRACTION	99
2.7744-2.8639	0.2538	142	0.2215	2652	X-RAY DIFFRACTION	98
2.8639-2.9663	0.2831	134	0.2241	2704	X-RAY DIFFRACTION	99
2.9663-3.085	0.2941	140	0.2254	2709	X-RAY DIFFRACTION	99
3.085-3.2254	0.2696	137	0.2144	2720	X-RAY DIFFRACTION	99
3.2254-3.3954	0.2401	149	0.1981	2721	X-RAY DIFFRACTION	100
3.3954-3.608	0.2282	143	0.1881	2742	X-RAY DIFFRACTION	100
3.608-3.8865	0.1873	138	0.1886	2674	X-RAY DIFFRACTION	98
3.8865-4.2774	0.1931	147	0.1638	2785	X-RAY DIFFRACTION	99
4.2774-4.8957	0.1587	149	0.1445	2767	X-RAY DIFFRACTION	100
4.8957-6.1659	0.1915	145	0.1759	2804	X-RAY DIFFRACTION	99
6.1659-46.859	0.2084	172	0.2121	2890	X-RAY DIFFRACTION	98

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	8.2663	1.0016	-1.3546	6.3294	-2.3554	4.6616	0.6418	0.2989	0.6305	-0.2876	-0.2681	1.3023	-0.2996	-0.4566	-0.2128	0.8487	0.2073	-0.4329	0.7601	-0.2723	1.1146	-14.1275	24.6274	19.1159
2	5.9875	-2.5211	0.5647	6.4367	-1.8762	6.575	0.135	0.0651	0.3946	-0.9042	-0.3926	0.8527	-0.5323	-0.4257	0.2087	0.6423	0.0101	-0.2242	0.3829	-0.1111	0.5279	-4.4684	15.5078	22.2705
3	3.9769	-0.8471	3.0064	3.2529	0.2265	7.8913	0.3977	0.7274	0.0644	-1.527	-0.2246	0.0236	1.2525	0.0903	-0.1537	0.9189	0.0578	-0.0451	0.4603	-0.0137	0.419	4.5373	4.069	14.9408
4	2.2292	-0.0182	-0.2782	1.9871	2.4101	8.7868	0.3877	0.5958	-0.3039	-1.2463	-0.4171	-0.797	2.3489	1.661	-0.226	1.5357	0.3891	-0.092	0.8554	0.0221	0.696	11.27	-5.302	10.8173
5	3.0169	-3.5404	-0.625	7.4023	2.7711	5.182	0.5902	0.2485	-0.0079	-2.4372	0.4023	-1.0956	1.1095	0.8643	-1.035	1.9027	0.2541	0.0551	1.1773	0.0821	0.861	18.5345	-6.0205	3.7523
6	4.9914	0.0892	-1.7154	0.8648	-0.6997	1.2006	0.2217	1.4988	-0.6071	-1.2024	-0.261	-0.1172	0.7945	-0.3165	-0.164	2.1741	0.2608	-0.1198	1.3404	-0.0506	0.7925	9.3559	-5.3602	-5.749
7	2.6313	0.717	0.7508	7.6362	1.0422	3.8012	0.0191	0.1978	0.3062	-0.6241	0.0056	0.0183	-0.0728	0.0186	-0.0247	0.2654	0.0062	-0.0235	0.2262	0.0579	0.3502	9.383	24.9534	36.8735
8	3.0936	-1.6143	-0.3679	8.4073	2.5445	3.861	-0.1553	0.1828	0.1872	-0.338	-0.0012	0.1229	-0.1423	0.0583	0.1506	0.2588	-0.0263	0.0449	0.2545	0.0848	0.3888	10.9032	25.2808	37.7154
9	8.469	-1.4071	5.4849	5.3783	-1.3343	7.6938	0.0416	-0.7255	0.1668	0.8011	-0.0973	-0.0918	-0.2841	-0.0503	-0.0363	0.3128	-0.0827	0.03	0.2671	-0.0029	0.4685	28.9906	36.919	67.1855
10	8.3589	-0.8664	3.3367	2.3307	-1.1975	2.9395	0.0653	0.0595	0.194	-0.0382	-0.0789	0.0016	-0.0028	0.0557	-0.0111	0.3021	0.0024	0.0442	0.2288	-0.012	0.5968	27.4972	36.3947	57.3361
11	6.7003	0.3888	4.4874	4.4947	-1.0918	7.359	-0.0163	-0.1391	0.1157	0.5232	-0.3755	-0.68	-0.2638	0.5597	0.3828	0.3047	-0.0509	0.0239	0.3253	0.0128	0.5777	37.5721	38.9118	65.0851
12	5.7002	-0.5901	4.388	3.956	-0.5702	6.2091	0.2457	-0.9433	-0.1909	0.138	-0.0081	0.3741	0.0147	-0.5736	-0.2073	0.2231	-0.029	0.0829	0.1954	0.037	0.3807	13.0712	5.788	56.8
13	1.2187	0.3203	0.8647	1.0801	-0.1991	1.9333	0.0383	0.0258	-0.072	-0.0599	-0.0057	-0.1166	0.0487	0.0161	-0.024	0.2228	0.0256	0.0355	0.2508	0.0072	0.3481	13.6747	5.7225	46.9436
14	1.2139	-1.1327	1.0859	6.1114	0.3868	3.2301	0.1214	-0.4034	0.5769	0.7975	-0.1405	0.153	-0.1556	-0.3126	0.0112	0.4949	0.0367	0.1469	0.3289	-0.0645	0.5935	22.7458	30.6848	72.8679
15	5.0487	-1.8297	-0.1349	8.3789	1.1784	5.9675	-0.123	-0.8156	0.3251	0.9355	0.0761	0.4955	-0.3468	-0.0445	0.1138	0.4841	-0.0027	0.1093	0.41	-0.0777	0.4827	20.4784	31.0179	73.7388
16	5.6672	0.9752	-3.8091	3.4822	1.9362	4.7492	-0.0829	1.8796	0.1303	-0.1999	-0.1907	0.7757	-0.2481	-1.1529	0.1868	1.4058	0.2351	-0.5737	1.1917	-0.0269	1.0223	-14.5454	22.8892	10.8824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 39 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 116 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 117 through 148 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 149 through 180 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 181 through 200 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 237 through 271 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 61 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 62 through 105 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 106 through 136 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 137 through 173 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 174 through 212 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 1 through 17 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 18 through 127 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 128 through 165 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 166 through 222 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 23 through 38 )

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