PDB-8tuz: Fab 857-2 in complex with OspA

ID or keywords:

Entry

Database: PDB / ID: 8tuz

Title

Fab 857-2 in complex with OspA

Components

Heavy chain of human monoclonal antibody 857-2
Light chain of human monoclonal antibody 857-2
Outer surface protein A

Keywords

IMMUNE SYSTEM / human monoclonal antibody / outer surface protein A

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 (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.186 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab 857-2 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 30, 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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PDBx/mmCIF format	8tuz.cif.gz	287.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8tuz.ent.gz	230.9 KB	Display	PDB format
PDBx/mmJSON format	8tuz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tuz_validation.pdf.gz	456 KB	Display	wwPDB validaton report
Full document	8tuz_full_validation.pdf.gz	460.8 KB	Display
Data in XML	8tuz_validation.xml.gz	28.4 KB	Display
Data in CIF	8tuz_validation.cif.gz	40.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tu/8tuz ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tuz	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 /

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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 human monoclonal antibody 857-2

L: Light chain of human monoclonal antibody 857-2

A: Outer surface protein A

hetero molecules

75 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)	42.847, 124.501, 144.349
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#3: Protein	Outer surface protein A Mass: 27037.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Gene: ospA / Production host: Escherichia coli B (bacteria) / References: UniProt: Q45040

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Antibody , 2 types, 2 molecules HL

#1: Antibody	Heavy chain of human monoclonal antibody 857-2 Mass: 24133.223 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 human monoclonal antibody 857-2 Mass: 23183.654 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 , 3 types, 297 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.59 Å³/Da / Density % sol: 52.49 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM hepes pH 7.5, 23% PEG 3350, and 200 mM sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 6, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.186→50 Å / Num. obs: 40753 / % possible obs: 100 % / Redundancy: 9.7 % / CC_1/2: 0.4 / Net I/σ(I): 3.9

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
2.2-2.24	9.5	2.102	2023	0.364	0.73	0.701	2.218	0.623	100
2.24-2.28	9.5	1.925	1986	0.313	0.69	0.647	2.034	0.645	100
2.28-2.32	9.3	1.916	1974	0.426	0.773	0.654	2.027	0.643	100
2.32-2.37	8.8	1.795	2038	0.397	0.754	0.634	1.906	0.648	100
2.37-2.42	8.6	1.635	1986	0.491	0.811	0.585	1.74	0.651	100
2.42-2.48	9.4	1.383	1988	0.534	0.834	0.47	1.463	0.679	100
2.48-2.54	10	1.256	2024	0.779	0.936	0.412	1.323	0.699	100
2.54-2.61	9.9	1.101	1997	0.828	0.952	0.361	1.159	0.72	100
2.61-2.69	9.8	0.929	2050	0.874	0.966	0.309	0.98	0.764	100
2.69-2.77	9.2	0.788	1983	0.882	0.968	0.271	0.835	0.85	100
2.77-2.87	9.6	0.675	2043	0.916	0.978	0.226	0.712	0.897	100
2.87-2.99	11	0.559	2016	0.954	0.988	0.175	0.586	0.962	100
2.99-3.12	10.6	0.416	2018	0.971	0.993	0.132	0.437	1.087	100
3.12-3.29	9.7	0.317	2049	0.979	0.995	0.106	0.334	1.288	100
3.29-3.49	9.2	0.24	2026	0.983	0.996	0.083	0.255	1.521	100
3.49-3.76	10.1	0.18	2040	0.99	0.997	0.059	0.19	1.76	100
3.76-4.14	9.7	0.139	2070	0.992	0.998	0.046	0.147	1.934	100
4.14-4.74	10.3	0.106	2093	0.995	0.999	0.035	0.112	2.106	100
4.74-5.97	10.3	0.097	2102	0.996	0.999	0.032	0.102	1.993	100
5.97-50	8.5	0.087	2247	0.996	0.999	0.032	0.093	2.515	99.7

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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: 2.186→39.885 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2391	2055	5.05 %
R_work	0.1767	-	-
obs	0.1797	40676	99.28 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.186→39.885 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5201	0	31	284	5516

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5337
X-RAY DIFFRACTION	f_angle_d	0.947	7212
X-RAY DIFFRACTION	f_dihedral_angle_d	3.142	4067
X-RAY DIFFRACTION	f_chiral_restr	0.057	833
X-RAY DIFFRACTION	f_plane_restr	0.005	909

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 (%)
2.1861-2.237	0.3264	124	0.2608	2283	X-RAY DIFFRACTION	90
2.237-2.2929	0.3352	148	0.2635	2528	X-RAY DIFFRACTION	100
2.2929-2.3549	0.3367	137	0.2532	2564	X-RAY DIFFRACTION	100
2.3549-2.4242	0.3459	113	0.2493	2548	X-RAY DIFFRACTION	100
2.4242-2.5024	0.3078	149	0.2292	2579	X-RAY DIFFRACTION	100
2.5024-2.5919	0.3037	135	0.2255	2527	X-RAY DIFFRACTION	100
2.5919-2.6956	0.31	144	0.2201	2575	X-RAY DIFFRACTION	100
2.6956-2.8183	0.2735	135	0.2106	2556	X-RAY DIFFRACTION	100
2.8183-2.9668	0.2609	143	0.2051	2570	X-RAY DIFFRACTION	100
2.9668-3.1526	0.2464	140	0.1948	2584	X-RAY DIFFRACTION	100
3.1526-3.3959	0.2907	124	0.1905	2602	X-RAY DIFFRACTION	100
3.3959-3.7374	0.2572	137	0.1624	2611	X-RAY DIFFRACTION	100
3.7374-4.2777	0.1947	141	0.1435	2647	X-RAY DIFFRACTION	100
4.2777-5.3874	0.1594	146	0.1242	2658	X-RAY DIFFRACTION	100
5.3874-39.885	0.2037	139	0.1608	2789	X-RAY DIFFRACTION	100

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	4.6723	0.9064	2.135	5.8953	-3.5733	7.7699	0.4457	0.0769	0.4454	-0.3362	-0.3978	-0.9775	-0.0392	0.6302	0.2556	0.3818	0.0966	0.1191	0.3046	0.0454	0.4213	70.7528	17.0278	60.1025
2	3.4167	-2.8399	1.7414	5.663	-1.4224	2.5344	0.0897	0.028	0.5509	-0.0339	-0.1992	-0.4632	-0.2992	0.0264	0.1291	0.3287	0.0445	0.0173	0.2814	-0.0031	0.2755	61.6922	22.4201	58.7703
3	3.9435	3.1971	4.1023	9.6494	5.5087	4.9584	0.1314	-0.2717	-0.7689	0.5842	-0.0449	0.2368	1.1141	-0.0927	-0.207	0.5097	-0.0403	0.0553	0.4214	0.0341	0.593	70.1404	-22.7715	58.6228
4	1.1634	-0.6926	-0.4204	5.6844	3.9463	4.8727	-0.09	-0.0381	-0.1663	0.0398	0.1324	-0.3404	-0.0143	0.1809	-0.0381	0.1867	-0.0013	-0.0046	0.388	0.0209	0.3502	73.0511	-12.2391	57.6125
5	2.2593	-1.1284	-0.1149	6.4194	0.4756	1.6303	0.0711	0.0859	-0.6682	-0.527	-0.332	1.3049	-0.1093	-0.5077	0.2266	0.4591	0.1673	-0.1345	0.5258	-0.0762	0.5784	43.206	6.0334	46.0751
6	1.3938	-0.7138	0.2455	4.8441	0.1074	1.7319	0.0846	0.1078	0.0354	-1.0222	-0.2556	0.315	-0.6447	-0.414	0.0862	0.6565	0.2787	-0.1437	0.4969	-0.094	0.3018	48.8489	14.0586	42.7646
7	2.6539	1.5703	0.4374	4.6968	1.237	4.1921	0.0651	-0.2186	0.0521	-0.3002	-0.5148	1.6213	-0.5912	-0.6209	0.5142	0.4289	0.166	-0.0553	0.4638	-0.0903	0.3637	47.5209	20.6451	54.6709
8	0.2511	0.1796	-0.4945	2.0669	0.7257	1.8428	-0.0352	0.019	-0.105	-0.2169	-0.0548	0.0229	-0.0255	-0.1172	0.0703	0.2077	0.0052	0.0089	0.3523	-0.0121	0.2774	54.9064	-11.9042	52.0676
9	2.6294	0.3359	1.4775	4.2945	-0.9657	8.424	0.2116	-0.1027	-0.3158	0.3017	-0.14	0.0276	0.3458	0.19	0.0368	0.239	0.012	0.033	0.2845	0.0069	0.3333	59.7065	-16.1921	62.9504
10	2.6744	0.0879	0.3475	6.4138	-1.3328	6.8797	-0.0893	-0.3154	-0.2465	0.934	0.1475	0.9925	0.4062	-0.6697	0.0217	0.2798	-0.0565	0.1166	0.4984	-0.0019	0.3686	54.6506	-14.6715	69.4912
11	6.9326	1.113	3.2452	8.7154	-2.8621	3.0119	-0.2398	0.6513	-0.0609	-0.8355	0.0344	-0.2144	-0.4103	0.5655	0.5059	0.3624	0.0252	-0.008	0.5107	-0.003	0.3117	58.4649	-8.6071	46.5031
12	4.121	-0.0242	1.7929	5.1242	-1.2423	3.0978	0.2296	-0.3997	-0.6079	0.7152	-0.1342	0.0406	0.3612	-0.4352	-0.1089	0.4042	-0.0302	0.0639	0.427	0.056	0.3169	57.3455	-21.9195	67.2279
13	3.541	-0.4994	0.8619	4.3461	1.7844	5.0601	-0.1863	0.0792	-0.8768	0.1026	-0.2325	0.804	0.4723	-0.3208	0.356	0.3576	0.0159	0.1681	0.2908	-0.0084	0.7878	39.379	28.6516	26.4455
14	2.6366	-2.5842	-0.5491	4.5115	1.5325	1.2867	-0.3789	-0.3332	-0.006	0.7569	0.2255	-0.0896	0.1445	0.083	0.0879	0.6054	0.2037	0.0907	0.4359	0.1153	0.4697	40.1035	46.4095	46.6475
15	4.0773	-1.4131	-0.7365	4.5112	3.0952	4.1868	-0.5165	-0.5086	-0.0706	0.6892	0.0553	0.5653	0.277	-0.2368	0.4226	0.6714	0.1925	0.1223	0.5637	0.0112	0.4763	22.6724	63.5	56.7484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 128 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 129 through 143 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 144 through 223 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 3 through 25 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 26 through 84 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 85 through 100 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 101 through 123 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 124 through 152 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 153 through 165 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 166 through 176 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 177 through 215 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 23 through 102 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 103 through 182 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 183 through 273 )

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