PDB-8tvj: Fab 227-1 in complex with OspA

ID or keywords:

Entry

Database: PDB / ID: 8tvj

Title

Fab 227-1 in complex with OspA

Components

Heavy chain of Fab 227-1
Light chain of Fab 227-1
Outer surface protein A

Keywords

IMMUNE SYSTEM/Membrane Protein / Human monoclonal antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-Membrane Protein complex

Function / homology

Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / 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: 3.168 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab 227-1 in complex with OspA
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	Aug 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tvj.cif.gz	277.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8tvj.ent.gz	225.9 KB	Display	PDB format
PDBx/mmJSON format	8tvj.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/tv/8tvj ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tvj	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

H: Heavy chain of Fab 227-1

L: Light chain of Fab 227-1

E: Outer surface protein A

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	109.578, 109.578, 316.123
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Antibody	Heavy chain of Fab 227-1 Mass: 24390.354 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	Light chain of Fab 227-1 Mass: 23239.787 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)
#3: Protein	Outer surface protein A Mass: 26722.105 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: P0CL66
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.19 Å³/Da / Density % sol: 61.45 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M triammonium citrate and 5% MPD.

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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: 3.15→50 Å / Num. obs: 16722 / % possible obs: 99 % / Redundancy: 5.7 % / CC_1/2: 0.47 / Net I/σ(I): 3.5

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
3.15-3.2	6	1.679	839	0.473	0.801	0.732	1.837	0.387	99.9
3.2-3.26	6	1.366	802	0.493	0.813	0.596	1.495	0.402	100
3.26-3.33	5.9	1.2	835	0.556	0.845	0.532	1.317	0.398	99.2
3.33-3.39	5.8	1.035	823	0.562	0.848	0.465	1.138	0.406	100
3.39-3.47	5.5	0.826	822	0.695	0.905	0.38	0.912	0.432	99.6
3.47-3.55	5	0.641	804	0.821	0.95	0.309	0.715	0.467	99
3.55-3.64	5.2	0.61	839	0.821	0.95	0.287	0.677	0.52	99.9
3.64-3.73	6.3	0.59	825	0.823	0.95	0.253	0.644	0.485	99.8
3.73-3.84	6.5	0.52	820	0.923	0.98	0.217	0.565	0.552	99.5
3.84-3.97	6.4	0.416	831	0.952	0.988	0.175	0.453	0.68	99.6
3.97-4.11	6.2	0.376	825	0.944	0.986	0.162	0.411	0.716	99.6
4.11-4.27	6	0.304	849	0.957	0.989	0.135	0.334	0.88	99.5
4.27-4.47	6	0.256	813	0.968	0.992	0.115	0.281	1.104	98.5
4.47-4.7	5.6	0.216	838	0.97	0.992	0.101	0.24	1.415	98.7
4.7-5	5.3	0.186	837	0.976	0.994	0.088	0.207	1.418	98.7
5-5.38	4.6	0.173	834	0.97	0.992	0.088	0.195	1.622	98.2
5.38-5.93	6.1	0.162	856	0.986	0.997	0.072	0.178	1.545	99.5
5.93-6.78	6.2	0.148	858	0.984	0.996	0.065	0.162	1.275	99
6.78-8.54	5.6	0.101	863	0.989	0.997	0.048	0.113	1.721	98
8.54-50	4.6	0.073	909	0.991	0.998	0.037	0.083	1.831	95.2

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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: 3.168→48.426 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2953	806	4.83 %
R_work	0.2354	-	-
obs	0.2385	16694	98.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.168→48.426 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5141	0	0	15	5156

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5234
X-RAY DIFFRACTION	f_angle_d	0.569	7085
X-RAY DIFFRACTION	f_dihedral_angle_d	2.539	3160
X-RAY DIFFRACTION	f_chiral_restr	0.045	822
X-RAY DIFFRACTION	f_plane_restr	0.004	893

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 (%)
3.1683-3.3667	0.3611	135	0.3335	2569	X-RAY DIFFRACTION	99
3.3667-3.6266	0.3704	139	0.2927	2600	X-RAY DIFFRACTION	100
3.6266-3.9914	0.328	128	0.2661	2639	X-RAY DIFFRACTION	100
3.9914-4.5686	0.2642	124	0.2244	2655	X-RAY DIFFRACTION	99
4.5686-5.7544	0.2706	141	0.2119	2653	X-RAY DIFFRACTION	99
5.7544-48.426	0.2849	139	0.2146	2772	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	1.6043	0.2178	0.893	2.6831	-2.1168	3.1221	-0.0127	-0.3406	0.165	0.4197	0.02	0.1951	-0.3158	-0.5146	0.0304	1.1021	0.2604	0.0794	1.0052	-0.0763	0.6146	-35.1739	-7.3583	-8.4721
2	4.3421	-0.4488	1.322	2.5666	0.5243	2.242	-0.7024	-0.0699	-1.4229	-0.6942	0.3015	0.3129	0.1503	0.6742	0.3957	0.8868	-0.1103	-0.1197	1.1995	0.325	0.8785	-15.7326	-33.8776	-21.6805
3	8.8407	1.8161	-4.0906	3.4165	0.399	5.401	0.3149	-0.9584	-0.3143	0.1885	0.2541	-0.3181	0.0704	0.977	-0.5516	0.8386	0.1651	-0.0373	0.9746	-0.0528	0.6989	-17.7737	-29.218	-15.5038
4	7.3067	-3.3509	-1.2193	3.9343	1.5116	5.4878	0.4034	1.5708	0.5591	0.1942	0.2264	-0.097	0.2055	-1.3023	-0.613	1.2848	0.1699	-0.0091	1.2692	0.1982	0.5581	-29.2854	-2.4119	-34.3101
5	7.405	-0.8451	-2.8571	5.3088	1.8305	3.024	0.244	0.1065	0.4392	-0.1714	0.031	0.1524	-0.6865	-0.922	-0.2361	1.0818	0.2693	-0.0245	1.0112	0.0867	0.5096	-27.9435	2.0689	-26.0478
6	1.7596	1.1157	-1.5271	6.5219	-4.8403	5.4532	0.15	0.3759	-0.4785	-0.7245	-0.0544	0.56	1.0661	0.0794	-0.0681	1.2057	0.0063	-0.1423	1.1036	-0.1502	0.825	-18.4995	-32.0929	-30.8738
7	6.9907	-1.0503	-2.9443	3.4647	-2.9018	6.5451	-0.3929	1.4161	-1.7784	0.1947	0.8881	-0.2474	-0.4256	1.0166	-0.5479	0.9819	0.2194	0.0284	1.4836	-0.2887	0.8706	-22.04	-29.5089	-31.9525
8	3.6905	3.0796	-1.9351	4.4939	-3.0802	5.2464	-0.5826	0.17	-0.8364	-0.8492	0.1114	-0.3452	1.0504	-0.0156	0.5542	1.6416	0.1501	0.1473	1.0254	-0.1584	0.9521	-18.5864	-40.6053	-32.9325
9	5.1213	-1.619	4.0747	3.4768	-5.0852	8.0068	-0.2488	0.6852	0.0555	0.6951	0.0053	0.1985	-0.9198	1.1325	0.1774	1.2183	0.0813	0.0297	1.6226	-0.0216	1.4587	-14.6025	29.5321	-28.254
10	3.9929	-0.185	-1.0738	6.6629	-0.4508	5.5193	-0.8207	0.0362	-0.4771	-0.2582	1.275	-3.7022	0.5037	1.0066	-0.5402	1.8532	-0.0603	-0.1053	1.3879	-0.1553	2.3379	-16.1864	24.6768	-25.9583
11	5.0043	0.5392	0.9678	8.6469	-8.8318	9.3654	0.2606	0.1333	-0.2006	0.7193	0.2638	0.3779	-0.1912	0.4029	-0.2394	1.4766	0.3206	-0.0629	1.1041	-0.2091	1.0523	-26.2253	22.6161	-17.7054
12	6.2143	-4.0541	1.3768	6.5067	-2.8809	5.8061	0.7369	-0.5618	0.9714	-0.3841	-0.5864	-0.2171	0.5997	0.9627	-0.0039	1.29	0.256	0.2423	0.8288	-0.0325	1.5212	-41.9508	28.8312	-10.5789
13	8.8149	-1.2438	-0.4058	5.8022	-1.3609	8.3794	-0.3223	-0.105	-2.634	-0.1198	-0.1805	0.9143	2.7459	0.2968	0.464	1.3165	0.0786	0.1737	0.6573	0.1592	1.3609	-56.7405	31.4791	-11.5562
14	6.5582	-0.8339	-0.4268	3.4806	-1.4549	3.45	-0.0124	0.0183	0.6075	-0.5496	0.1431	-0.3308	0.2415	-0.5106	-0.2782	1.2708	0.1607	0.1224	1.0105	-0.0997	1.225	-63.5176	44.5891	-16.0976

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 139 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 140 through 158 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 159 through 227 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 1 through 18 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 19 through 104 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 105 through 150 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 151 through 172 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 173 through 213 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 26 through 58 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 59 through 74 )
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 75 through 126 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 127 through 166 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 167 through 203 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 204 through 273 )

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