PDB-9byf: Fab 212-55 in complex with OspA

ID or keywords:

Entry

Database: PDB / ID: 9byf

Title

Fab 212-55 in complex with OspA

Components

221-55 Fab Heavy Chain
221-55 Fab Light Chain
Outer surface protein A

Keywords

IMMUNE SYSTEM/ANTIGEN / Fab-antigen complex / IMMUNE SYSTEM / IMMUNE SYSTEM-ANTIGEN 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 (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab 212-55 in complex with OspA
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	May 23, 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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Validation report

Summary document	9byf_validation.pdf.gz	459.7 KB	Display	wwPDB validaton report
Full document	9byf_full_validation.pdf.gz	467.8 KB	Display
Data in XML	9byf_validation.xml.gz	28.6 KB	Display
Data in CIF	9byf_validation.cif.gz	36.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/9byf ftp://data.pdbj.org/pub/pdb/validation_reports/by/9byf	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: 221-55 Fab Heavy Chain

L: 221-55 Fab Light Chain

A: Outer surface protein A

hetero molecules

75.9 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)	101.120, 162.416, 126.785
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	21
Space group name H-M	C222
Space group name Hall	C22

Components on special symmetry positions

ID	Model	Components
1	1	H-443- HOH
2	1	H-451- HOH
3	1	L-404- HOH

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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 (Lyme disease spirochete) Strain: B31 / Gene: ospA, BB_A15 / Production host: Escherichia coli B (bacteria) / References: UniProt: P0CL66

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Antibody , 2 types, 2 molecules HL

#1: Antibody	221-55 Fab Heavy Chain Mass: 24533.389 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	221-55 Fab Light Chain Mass: 23449.910 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, 125 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.44 Å³/Da / Density % sol: 64.28 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5, 23% PEG 3350, and 200 mM NaCl

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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: Mar 12, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.85→50 Å / Num. obs: 24587 / % possible obs: 99.6 % / Redundancy: 9.9 % / B_iso Wilson estimate: 50.82 Å² / R_merge(I) obs: 0.353 / Net I/σ(I): 2.6

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
2.85-2.9	10.1	1.911	1218	0.353	0.722	0.627	2.015	0.693	99.8
2.9-2.95	9.8	1.727	1200	0.47	0.8	0.574	1.823	0.708	99.9
2.95-3.01	9	1.502	1229	0.553	0.844	0.523	1.593	0.7	99.9
3.01-3.07	9.1	1.324	1217	0.642	0.884	0.459	1.404	0.704	99.8
3.07-3.14	9.2	1.264	1201	0.67	0.896	0.435	1.339	0.742	99.7
3.14-3.21	9.3	1.112	1206	0.767	0.932	0.379	1.177	0.783	99.5
3.21-3.29	9.2	0.942	1218	0.816	0.948	0.324	0.998	0.802	99.6
3.29-3.38	8.9	0.807	1228	0.861	0.962	0.281	0.856	0.845	99.6
3.38-3.48	8.2	0.655	1188	0.856	0.96	0.237	0.699	0.926	99
3.48-3.59	9.8	0.603	1246	0.905	0.975	0.2	0.637	0.903	99.9
3.59-3.72	11.3	0.532	1208	0.954	0.988	0.164	0.557	0.911	99.6
3.72-3.87	11.2	0.429	1240	0.976	0.994	0.134	0.45	0.938	100
3.87-4.04	10.8	0.365	1219	0.976	0.994	0.116	0.384	0.999	99.8
4.04-4.26	10.1	0.271	1225	0.983	0.996	0.089	0.286	1.109	99.9
4.26-4.52	11	0.212	1241	0.987	0.997	0.067	0.223	1.207	99.8
4.52-4.87	10.1	0.185	1226	0.99	0.997	0.061	0.195	1.297	99.5
4.87-5.36	9	0.17	1231	0.988	0.997	0.059	0.181	1.246	98.9
5.36-6.14	11.8	0.186	1256	0.991	0.998	0.056	0.194	1.086	99.9
6.14-7.73	10.9	0.141	1269	0.991	0.998	0.045	0.148	1.202	99.8
7.73-50	9.5	0.083	1321	0.996	0.999	0.028	0.088	1.493	98.4

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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: 2.85→47.73 Å / SU ML: 0.3596 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2884	1264	5.15 %
R_work	0.2302	23298	-
obs	0.2331	24562	98.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→47.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4673	0	12	116	4801

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0016	4781
X-RAY DIFFRACTION	f_angle_d	0.4463	6480
X-RAY DIFFRACTION	f_chiral_restr	0.0405	749
X-RAY DIFFRACTION	f_plane_restr	0.0037	828
X-RAY DIFFRACTION	f_dihedral_angle_d	4.1785	661

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 (%)
2.85-2.96	0.3222	143	0.3031	2408	X-RAY DIFFRACTION	93.96
2.96-3.1	0.3626	147	0.2905	2581	X-RAY DIFFRACTION	99.74
3.1-3.26	0.3313	142	0.2778	2553	X-RAY DIFFRACTION	99.48
3.26-3.46	0.3549	142	0.2687	2570	X-RAY DIFFRACTION	99.23
3.46-3.73	0.2757	125	0.2307	2606	X-RAY DIFFRACTION	99.74
3.73-4.11	0.2627	134	0.2111	2611	X-RAY DIFFRACTION	99.75
4.11-4.7	0.2332	166	0.1786	2581	X-RAY DIFFRACTION	99.67
4.7-5.92	0.2665	137	0.2034	2649	X-RAY DIFFRACTION	99.39
5.92-47.73	0.2885	128	0.2312	2739	X-RAY DIFFRACTION	98.86

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	3.24319125142	1.90938947743	2.82857148949	4.11483013857	2.76818392138	5.79619151164	-0.117357142844	0.111648770446	0.350274646673	-0.149601692358	-0.165561399126	0.635942831918	-0.0013416739861	-0.287799861996	0.354126557562	0.212418171424	-0.04225287806	0.0549919164941	0.136081517817	0.124136591091	0.836696336303	-12.2934359254	-13.8659853196	45.3137677081
2	1.34729485622	1.23621201041	-0.246850148926	3.54975637131	1.03643520461	0.993089113253	-0.420085583309	0.413061732758	-0.12139742968	-0.826000884091	0.214383262477	0.0510951636149	-0.488375438412	0.104775858448	0.0612300318365	0.390296059743	-0.360720074714	0.0371512675523	0.29189508063	-0.100568250461	0.784594343131	-10.7452540654	-13.1041813437	32.0471284775
3	3.31367312795	-0.192940770309	1.91504795775	3.40723373844	1.79845524524	3.94889162377	-0.210207686525	-0.119356495305	0.466708066209	1.46505235746	0.318557328593	1.23215872408	0.160759390496	0.662193589649	-0.220774645282	1.54421426329	-0.68916999704	0.272930871622	1.93542130952	-0.0483701970353	0.778064810942	-20.3479655192	-6.80746736925	113.923881276
4	3.84156226828	1.11249012327	2.4413467603	2.66594245176	0.976253192185	4.97365794653	0.217583550682	-1.0799857907	0.239776286777	0.37432751345	-0.34855027941	-0.155823473233	-0.178118404925	-0.0545380145024	0.264145158954	0.39706139558	-0.149536522651	0.108546650672	0.856955512103	-0.23754714778	0.919730699867	-36.533591451	-7.26765216894	97.6091257819
5	4.19415408315	1.58698611281	-1.89053235163	0.901167445391	-0.529758858822	1.98294729103	0.152812041647	-0.220220142978	-0.236861869667	0.251236025508	-0.116830109635	0.663177037978	-0.0284683708584	-0.312658786941	-0.0935487454759	0.167780504593	-0.0543475043689	0.0955958493971	0.747042313279	-0.188979766007	0.841025295737	-54.301211009	-19.1393312794	87.9936728762
6	2.44653571696	-0.647522321393	1.95899382368	2.58383985271	-0.96706462587	5.60216159542	0.290573108874	-0.00973101668542	-0.428826611149	0.0207425760319	-0.16682968385	0.180285283439	0.270817261836	0.492415855939	-0.17630119169	0.233142566233	-0.0280305099731	0.203790828535	0.325689662858	-0.0365002213445	0.916394957291	-29.4506389671	-34.6899991505	63.3645330781
7	2.11224566276	0.607312025163	-0.283253968746	0.269973983792	0.0852360763462	1.33679030167	-0.141004596055	-0.413247390122	-0.38518693343	0.0918832003931	-0.0298511720857	0.255595371471	0.251153869701	-0.0524761295873	0.265397522959	0.102299518582	-0.0624235500327	0.184588976442	0.381659716892	0.158948840227	0.822399278038	-34.1850054171	-28.4039128407	72.9870039038
8	2.51315354392	1.40054371196	1.80873144903	2.58180041274	-0.249907741715	7.0110214938	-0.0881788763848	0.0905022798306	-0.47977822858	0.275173820468	-0.110489770991	0.250796077344	0.858476899711	-0.293009222526	0.0594394422038	0.324217120277	-0.0233022022326	0.212515636993	0.29340007088	0.0102532307975	0.840401892084	-38.9066931833	-32.4035981334	69.5136229487
9	1.74049887623	0.519954532563	0.966275900372	0.909299669237	1.48982596863	2.43183829553	0.171625779257	-0.381063718757	-0.349597332082	0.267040335749	0.0437276384044	-0.238328172535	0.302178186655	0.0257893448364	-0.250525846634	0.311109260296	0.000288251070003	0.106333419876	0.281785279911	0.0465604765444	1.07112337031	-30.4711080117	-25.8557077517	70.2746471122
10	0.395995427257	0.759912193012	-0.0667817171277	1.48172009587	-0.293548706213	1.13714687396	0.0380275233527	0.0677454082282	-0.539885468412	-0.281614133061	0.00174974347494	-0.622035582681	-0.151961914601	0.301508276407	-0.0154061665827	0.191793680858	-0.0827818867778	0.13177218484	0.234824864171	-0.153072914315	0.776344535834	-18.6117683271	-30.9856231476	41.3673976699
11	1.51051186448	0.902234535056	0.317351760026	0.773724753367	0.209329329031	0.670834420251	-0.109896090711	0.171192428022	-0.0562366447043	0.0397426954184	-0.0575225407621	-0.486707577764	-0.0385313542608	0.0950577976535	0.102877515101	0.150044571384	-0.103880999942	0.00044974457812	0.275720827595	-0.0348513646885	1.16905865373	-10.1886567947	-27.1002369094	45.4031137816
12	5.28721171683	0.841264725582	-0.461519207686	0.228708371735	-0.191449068124	0.182693658478	0.0960485980943	-0.0732825953848	0.239965408004	-0.389797724868	-0.160238354853	-0.563530712765	-0.0298422072422	0.243241530967	0.0449964859457	0.243197047605	0.0560389314696	0.112333267615	0.334299756439	0.00452088580018	1.18293981935	-1.06009014946	-33.3853043048	43.379910436
13	3.65319672462	-1.11152075257	1.08392558158	3.83412045157	0.259353726901	2.5225997025	0.112176744563	0.533521855208	-0.120257075962	-0.264559682922	0.158695667575	-0.595704462085	0.0415259592464	0.375643383512	-0.05515981392	0.251525539848	-0.194279551964	0.0639609495238	0.347533298228	-0.132314718701	0.603409350417	-8.57728060396	-36.3847090872	41.0066737908
14	0.498069516435	-0.21779265112	-1.01530105673	0.119352926907	0.386015559071	2.20264973613	0.0654745765225	-0.387572055147	0.174744014354	-0.0468403413166	0.0235313736742	-0.0221228499565	-0.23388523467	0.150310668373	0.175866211381	-0.00590327584647	0.0231443208057	0.0431216612951	0.217216478784	0.092361191743	0.674603655156	-19.5285357621	-6.03183777648	67.4440791699
15	2.73782742909	-1.43565079433	-1.64044151673	0.79355894811	1.06871630797	2.01264538036	0.26700697804	0.151079139605	0.958782491962	-0.00523351784126	-0.0950252081909	0.07783392486	-0.360490783558	-0.0522994761995	-0.208390912307	0.150073794477	0.0376925876613	0.107195032221	0.287051363488	-0.0614250824924	0.909006352215	-27.0444236212	-8.90920823984	74.3875849992
16	1.94420979851	0.516103788183	-0.953685473412	0.819264490143	-0.259306292151	1.61563372518	0.170313801997	-0.382530808977	0.181758955877	0.170501065883	-0.245128702078	-0.0961249194983	-0.121910027602	-0.0540917696845	0.158168335367	0.0956428574285	-0.0296495475373	-0.0101233945897	0.465301802397	-0.081874679008	0.890271875725	-19.4324285658	-12.9204521899	77.2958095268
17	0.438662313324	0.02317411761	-0.24744429823	1.04371023967	0.218743612433	0.408214252301	-0.0792996107646	-0.0386481188352	-0.380913563982	0.242818331584	-0.0479980454786	0.0428298668311	0.0708191794593	0.0393312586537	-0.000327728789262	0.186501333324	0.0324280415946	-0.0777344901315	0.204291104004	-0.000321782332718	0.981535842124	-18.1049926286	-11.7887506334	67.4291446779
18	2.44568922273	2.8360866959	0.855449770374	3.88855544234	0.0154673139847	1.85746602222	-0.311270329669	0.247957484908	0.0986098764496	-0.663133246655	0.465826861717	-0.0520840909602	0.0805111061302	-0.207854371114	0.0157241261589	0.189992367624	-0.0964847034661	0.0242426333342	0.41368917252	-0.0564492667071	0.9045013303	-10.3396570221	-16.9633216868	37.9570066861

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'L' and (resid 152 through 175 )	L	B	152 - 175	152 - 175
2	2	chain 'L' and (resid 176 through 213 )	L	B	176 - 213	176 - 213
3	3	chain 'A' and (resid 88 through 108 )	A	C	88 - 108	1 - 21
4	4	chain 'A' and (resid 109 through 203 )	A	C	109 - 203	22 - 116
5	5	chain 'A' and (resid 204 through 273 )	A	C	204 - 273	117 - 186
6	6	chain 'H' and (resid 1 through 17 )	H	A	1 - 17	1 - 17
7	7	chain 'H' and (resid 18 through 60 )	H	A	18 - 60	18 - 60
8	8	chain 'H' and (resid 61 through 83 )	H	A	61 - 83	61 - 83
9	9	chain 'H' and (resid 84 through 118 )	H	A	84 - 118	84 - 118
10	10	chain 'H' and (resid 119 through 143 )	H	A	119 - 143	119 - 136
11	11	chain 'H' and (resid 144 through 197 )	H	A	144 - 197	137 - 190
12	12	chain 'H' and (resid 198 through 209 )	H	A	198 - 209	191 - 202
13	13	chain 'H' and (resid 210 through 223 )	H	A	210 - 223	203 - 216
14	14	chain 'L' and (resid 1 through 18 )	L	B	1 - 18	1 - 18
15	15	chain 'L' and (resid 19 through 39 )	L	B	19 - 39	19 - 39
16	16	chain 'L' and (resid 40 through 76 )	L	B	40 - 76	40 - 76
17	17	chain 'L' and (resid 77 through 114 )	L	B	77 - 114	77 - 114
18	18	chain 'L' and (resid 115 through 151 )	L	B	115 - 151	115 - 151

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