PDB-9c24: Fab F946 in complex with OspCB

ID or keywords:

Entry

Database: PDB / ID: 9c24

Title

Fab F946 in complex with OspCB

Components

F946 Fab Heavy Chain
F946 Fab Light Chain
Outer surface protein C

Keywords

IMMUNE SYSTEM / Fab-antigen complex

Function / homology

Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / Outer surface protein C

Function and homology information

Biological species

Homo sapiens (human)

Borreliella burgdorferi (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab F946 in complex with OspCB
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	May 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9c24.cif.gz	457.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9c24.ent.gz	377.7 KB	Display	PDB format
PDBx/mmJSON format	9c24.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9c24_validation.pdf.gz	472.4 KB	Display	wwPDB validaton report
Full document	9c24_full_validation.pdf.gz	493.4 KB	Display
Data in XML	9c24_validation.xml.gz	47.2 KB	Display
Data in CIF	9c24_validation.cif.gz	61.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c2/9c24 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/9c24	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: F946 Fab Heavy Chain

L: F946 Fab Light Chain

A: F946 Fab Heavy Chain

B: F946 Fab Light Chain

C: Outer surface protein C

D: Outer surface protein C

131 kDa, 6 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)	77.794, 96.459, 188.671
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	F946 Fab Heavy Chain Mass: 24591.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	F946 Fab Light Chain Mass: 23429.057 Da / Num. of mol.: 2 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 C Mass: 17399.859 Da / Num. of mol.: 2 / Fragment: residues 38-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Strain: B31 / Gene: ospC / Production host: Escherichia coli B (bacteria) / References: UniProt: Q44977
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.71 Å³/Da / Density % sol: 54.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 210 mM calcium chloride and 18% PEG 3350

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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 S 9M / Detector: PIXEL / Date: Oct 5, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 35099 / % possible obs: 98.8 % / Redundancy: 11.2 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.124 / R_pim(I) all: 0.038 / R_rim(I) all: 0.13 / Χ²: 0.703 / Net I/σ(I): 4.5

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
2.8-2.85	7.3	0.763	1513	0.655	0.89	0.288	0.82	0.343	85.9
2.85-2.9	7.8	0.757	1623	0.66	0.892	0.279	0.812	0.35	94.4
2.9-2.96	8.7	0.657	1692	0.776	0.935	0.232	0.7	0.353	96.7
2.96-3.02	9.3	0.66	1746	0.8	0.943	0.225	0.699	0.369	99.4
3.02-3.08	10	0.615	1747	0.858	0.961	0.203	0.649	0.381	99.9
3.08-3.15	10.6	0.534	1737	0.908	0.976	0.171	0.562	0.392	99.8
3.15-3.23	10.5	0.432	1754	0.948	0.987	0.139	0.455	0.42	99.8
3.23-3.32	11.3	0.41	1751	0.956	0.989	0.126	0.43	0.433	100
3.32-3.42	11.8	0.328	1756	0.974	0.993	0.099	0.343	0.485	99.9
3.42-3.53	11.3	0.254	1765	0.98	0.995	0.078	0.266	0.545	99.9
3.53-3.65	12.7	0.213	1744	0.988	0.997	0.062	0.222	0.579	99.9
3.65-3.8	12.9	0.191	1764	0.991	0.998	0.055	0.199	0.617	99.9
3.8-3.97	12.8	0.151	1763	0.992	0.998	0.044	0.158	0.701	100
3.97-4.18	12.8	0.13	1771	0.995	0.999	0.038	0.135	0.786	99.9
4.18-4.44	12.8	0.107	1787	0.996	0.999	0.031	0.111	0.923	100
4.44-4.79	12.7	0.097	1790	0.997	0.999	0.028	0.101	1	100
4.79-5.27	12.5	0.09	1794	0.997	0.999	0.026	0.094	0.963	100
5.27-6.03	11.4	0.09	1818	0.997	0.999	0.028	0.094	0.97	100
6.03-7.59	11.5	0.077	1830	0.997	0.999	0.023	0.081	0.985	99.9
7.59-50	12.3	0.051	1954	0.999	1	0.015	0.054	1.579	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→48.91 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2881	1688	4.82 %
R_work	0.234	-	-
obs	0.2366	35013	98.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.8→48.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8654	0	0	72	8726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8813
X-RAY DIFFRACTION	f_angle_d	0.718	11938
X-RAY DIFFRACTION	f_dihedral_angle_d	6.934	1187
X-RAY DIFFRACTION	f_chiral_restr	0.042	1393
X-RAY DIFFRACTION	f_plane_restr	0.006	1495

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 (%)
2.8-2.89	0.4133	123	0.378	2360	X-RAY DIFFRACTION	85
2.89-2.98	0.3899	142	0.3297	2654	X-RAY DIFFRACTION	96
2.98-3.09	0.3718	144	0.3176	2781	X-RAY DIFFRACTION	100
3.09-3.21	0.3617	138	0.2775	2791	X-RAY DIFFRACTION	100
3.21-3.36	0.3595	139	0.2887	2794	X-RAY DIFFRACTION	100
3.36-3.53	0.3277	140	0.2855	2785	X-RAY DIFFRACTION	100
3.53-3.75	0.3011	141	0.2582	2816	X-RAY DIFFRACTION	100
3.75-4.04	0.2997	141	0.2202	2796	X-RAY DIFFRACTION	100
4.04-4.45	0.2561	161	0.1973	2811	X-RAY DIFFRACTION	100
4.45-5.09	0.2357	146	0.1778	2855	X-RAY DIFFRACTION	100
5.09-6.41	0.2762	136	0.2185	2887	X-RAY DIFFRACTION	100
6.42-48.91	0.2417	137	0.211	2995	X-RAY DIFFRACTION	99

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	4.2826	-1.2914	-0.3566	4.5882	1.341	2.2955	0.1375	0.3476	0.181	-0.0488	-0.1085	0.5884	-0.1461	-0.3421	-0.0116	0.2615	-0.0332	0.0563	0.4028	0.0418	0.4046	-20.8865	41.2206	-33.8012
2	5.6765	-1.3702	-0.8435	7.0819	0.4299	3.6061	-0.475	-1.0177	-0.6503	2.1306	-0.0267	0.1361	-0.3094	-0.6812	0.4768	0.9225	0.0532	0.4483	0.8753	-0.087	1.1494	-37.129	47.0272	-6.6873
3	9.6337	-1.595	2.7955	7.2635	-1.5212	8.8204	0.0178	-0.6908	0.2045	2.5208	-0.2545	0.801	-0.4268	-0.4864	0.203	1.1608	0.0437	0.3553	0.5668	-0.0173	0.837	-32.6832	46.1889	-11.3174
4	4.6651	-0.3022	0.188	2.3744	0.2358	3.1986	-0.0408	-0.2428	0.2103	1.7982	-0.0605	0.8944	0.114	-0.0182	0.1619	1.2201	0.0072	0.5469	0.6666	-0.0676	1.043	-33.3972	40.9788	-8.1908
5	4.6443	0.5356	-4.5059	0.1794	-0.6231	4.8122	-0.3878	-1.7549	0.7147	2.5983	-0.6374	-0.4053	-0.3987	1.1265	0.8373	2.7478	0.0146	0.0991	1.041	-0.1541	0.8745	-29.1546	40.364	6.0879
6	6.639	-0.2683	0.7923	4.3141	0.5109	4.1218	-0.0095	-0.6145	1.3038	2.0807	-0.5555	1.0414	-0.0096	-0.3457	0.3592	1.3809	0.0306	0.5386	0.7343	-0.1289	1.2126	-28.7932	51.8256	-9.0414
7	5.0511	-0.5092	-0.0105	4.5777	0.3352	3.2518	-0.2885	0.8055	-0.838	0.5897	0.0783	0.8541	0.4896	-1.0796	0.1022	0.6342	-0.3008	0.3461	0.6295	-0.2361	1.0868	-31.2292	19.3323	-28.9415
8	4.9743	-1.9983	-0.5879	4.7285	-3.8517	4.2835	-0.9841	0.4524	-1.175	1.4561	-0.1691	0.6508	1.7397	-0.2334	0.5718	1.2636	-0.2498	0.43	0.4822	-0.0254	0.8699	-25.8232	13.156	-24.8458
9	3.5072	-1.5597	-2.0625	7.1179	1.3516	4.9406	-0.1731	-0.0156	-0.5424	0.8166	0.1021	0.4185	0.9407	-0.3052	0.0529	0.4198	-0.1373	0.0775	0.3629	-0.0583	0.4989	-20.5229	22.0843	-28.5646
10	1.4542	0.6979	0.2768	0.7332	-0.1302	0.3661	-1.5972	-0.6398	0.5215	1.9196	0.3123	1.4942	0.2354	-0.1992	0.0943	1.5592	-0.1053	1.2961	0.751	0.0573	0.9459	-38.3818	34.1258	-2.1185
11	4.0672	-1.25	1.8369	3.8581	3.3606	5.5494	0.1279	-1.2593	-0.9235	-0.7058	-0.928	-0.7064	1.1933	-0.8131	0.7621	1.7491	-0.2151	0.8623	1.1235	0.0694	1.3774	-43.3513	30.0872	-2.8069
12	4.7413	-0.9391	1.2957	1.4657	0.4213	0.8315	-0.2692	-1.2731	0.5262	-0.5957	0.0178	0.5091	0.3047	-0.127	0.134	1.676	-0.3165	0.886	0.9776	-0.1307	1.255	-43.6797	35.4429	-4.4491
13	3.0357	-1.8536	0.7557	5.1164	1.0085	1.5666	-0.2172	-0.4575	-0.8522	-0.6184	0.3344	-0.2729	0.6892	-1.4019	-0.0633	1.3807	-0.0925	0.6647	1.5115	0.1448	1.3433	-48.8008	29.5952	4.2491
14	2.6741	1.0508	2.9848	3.2437	0.7723	6.9747	0.0688	-0.2237	-0.1491	-0.225	0.0187	0.0184	-0.22	-0.6639	-0.0798	0.2526	0.0342	0.1046	0.3421	0.0165	0.3954	-5.8567	4.5728	-71.6841
15	1.8993	0.8627	0.356	0.8139	-0.0728	3.2504	-0.0088	0.4354	0.047	-0.5284	0.3365	-0.1099	-0.1551	0.095	-0.3435	0.571	0.0649	0.1243	0.4699	0.0034	0.4328	-3.5271	7.7773	-87.5333
16	1.6879	1.316	1.142	6.3516	-2.6535	4.4867	0.0323	1.6526	-0.8297	-0.2299	0.0598	-1.0784	-0.665	0.603	-0.1385	0.9311	-0.1206	0.4491	1.0368	-0.0391	0.9896	0.7023	6.3909	-105.0918
17	7.5073	-3.4839	0.0681	2.9166	1.2492	1.3246	0.0436	0.4593	-1.3288	-1.0855	-0.6546	-0.2374	0.6595	1.7237	0.6534	0.9558	-0.209	0.3459	1.3438	-0.172	1.1166	5.4612	0.8246	-111.2593
18	2.6758	0.2294	0.5787	2.7396	-0.5669	7.6756	-0.0614	0.3983	1.1033	-1.0861	0.1776	-0.4415	-1.743	-0.1935	-0.1348	1.0345	0.0582	0.2277	0.4708	0.0608	0.6567	-0.3402	28.224	-77.9945
19	1.3666	0.3102	0.081	0.3026	0.505	3.602	-0.405	0.6817	0.3764	-1.4428	0.4555	0.095	-0.0792	-0.2401	-0.0658	1.8784	-0.0375	0.0823	0.6755	0.1172	0.5636	-2.2999	19.8836	-94.0984
20	1.5454	-1.6442	1.2947	1.6335	-0.9005	4.1558	-0.128	0.3585	0.1164	-1.6673	0.2569	-0.0059	-0.5917	-0.1946	-0.2124	2.2988	-0.2288	0.0723	1.105	0.1278	0.6483	-9.1933	17.755	-112.101
21	5.7605	-1.7173	-5.0735	2.0088	1.2081	4.526	0.4126	0.2479	0.5726	0.2288	0.5362	1.4769	0.6999	-0.7086	-0.8099	0.4073	0.0679	0.1841	0.7026	0.0286	0.7694	-16.0514	18.7304	-49.9559
22	2.3599	0.5403	1.721	2.4761	0.9013	2.2264	0.4957	-0.0361	2.0121	0.312	-0.3584	-0.722	0.0375	0.4974	-0.0964	0.4182	0.0461	0.0127	0.5915	-0.1255	1.1623	20.1867	24.647	-43.3291
23	7.0537	1.2964	4.9574	6.1336	0.5273	6.4212	0.448	-2.0985	-0.1204	0.5471	-0.3693	-0.4608	0.6721	-0.331	-0.013	0.5097	-0.0155	-0.0735	0.6149	-0.0572	0.3803	17.4137	15.8516	-35.6853
24	4.2118	-1.231	2.8355	9.4514	0.7473	2.1862	0.9952	-0.8111	-1.681	0.0669	-0.0911	1.9035	1.306	-2.3752	-0.7452	0.7866	-0.3167	-0.3289	1.2136	-0.0079	0.8643	-1.4187	9.1131	-45.9551
25	7.3244	-1.9586	3.953	4.0718	-0.4576	6.2984	0.8985	0.0785	-1.0748	0.5927	-0.1147	-0.8981	1.313	0.8313	-0.7917	0.6693	0.1677	-0.1878	0.6163	-0.1379	0.8888	23.2482	9.3104	-39.6149
26	1.858	-0.9736	1.7591	3.2037	3.4904	8.8762	0.7644	0.9145	-1.0795	-0.1213	0.1677	-1.0228	1.5079	0.1303	-0.8237	0.6316	0.0074	0.0744	0.7009	-0.0677	1.1184	29.8177	13.1228	-47.3829
27	3.7998	-0.7926	4.8413	2.4938	-0.6942	5.8219	1.205	0.7217	-0.6357	0.0971	-0.5391	-0.3182	0.566	-0.0307	-0.529	0.3437	0.0785	0.0473	0.5427	-0.0571	0.3939	5.421	14.1439	-52.6241
28	2.8997	-2.2013	3.6279	3.3571	-2.695	3.7376	-0.1681	-0.0384	0.9334	-0.4058	-0.3745	-0.8695	0.4455	0.2852	0.3767	0.3321	0.001	0.0867	0.5789	-0.127	0.6044	3.8592	28.0509	-46.111
29	2.7971	-2.3407	3.327	3.9206	-1.5194	4.7673	0.3642	-1.1132	0.4514	0.1152	0.2122	-0.7128	0.4281	-0.049	-0.2981	0.421	-0.0435	0.0211	0.9082	-0.1579	1.0416	22.4077	26.2011	-36.8831
30	3.7004	-0.1961	3.3909	1.0335	-0.7264	3.3414	-0.3654	-0.351	2.0607	-0.0059	0.3097	-0.8031	-0.5162	0.2208	0.1731	0.4013	-0.096	0.0485	0.7355	-0.2978	2.1355	21.6041	39.2109	-37.5519
31	0.278	-1.1881	0.3891	8.6048	-1.3491	3.3478	-0.2801	-1.5559	1.4883	0.8052	0.696	-1.4417	-0.3506	1.2831	-0.2933	0.5126	-0.0092	-0.0883	1.1622	-0.4897	1.0551	22.9773	33.7246	-25.5843
32	8.6625	3.779	5.9093	4.1107	2.6519	8.3209	0.4585	-0.9349	1.6553	0.228	-0.3885	-0.4095	0.1016	-0.0163	0.1922	0.3427	-0.1223	0.1452	0.6779	-0.3058	0.7772	-0.7753	33.9434	-40.6766

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 119 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 120 through 153 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 154 through 164 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 165 through 187 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 188 through 205 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 206 through 217 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid -1 through 12 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 13 through 23 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 24 through 99 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 100 through 126 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 127 through 147 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 148 through 186 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 187 through 208 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 83 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 84 through 155 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 156 through 194 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 195 through 218 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 0 through 73 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 74 through 126 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 127 through 208 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 40 through 48 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 49 through 93 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 94 through 113 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 114 through 120 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 121 through 155 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 156 through 170 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 171 through 200 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 41 through 75 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 76 through 120 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 121 through 151 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 152 through 170 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 171 through 202 )

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