PDB-9cfd: Fab 8C1 in complex with OspCA peptide P15 (residues 132-146)

ID or keywords:

Entry

Database: PDB / ID: 9cfd

Title

Fab 8C1 in complex with OspCA peptide P15 (residues 132-146)

Components

(Monoclonal 8C1 Fab ...) x 2
Outer surface protein C

Keywords

IMMUNE SYSTEM / Anti-OspA antibody

Function / homology

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

Function and homology information

Biological species

Homo sapiens (human)

Borreliella burgdorferi B31 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Fab 8C1 in complex with OspCA peptide P15 (residues 132-146)
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	Jun 27, 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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Download

PDBx/mmCIF format	9cfd.cif.gz	326 KB	Display	PDBx/mmCIF format
PDB format	pdb9cfd.ent.gz	221.2 KB	Display	PDB format
PDBx/mmJSON format	9cfd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cfd_validation.pdf.gz	458.3 KB	Display	wwPDB validaton report
Full document	9cfd_full_validation.pdf.gz	461.7 KB	Display
Data in XML	9cfd_validation.xml.gz	26.6 KB	Display
Data in CIF	9cfd_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/9cfd ftp://data.pdbj.org/pub/pdb/validation_reports/cf/9cfd	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: Monoclonal 8C1 Fab Heavy Chain

L: Monoclonal 8C1 Fab Light Chain

P: Outer surface protein C

hetero molecules

49.9 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)	106.440, 106.440, 71.344
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅
Space group name Hall	P6₅

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide	Outer surface protein C / pC / P23 Mass: 1764.972 Da / Num. of mol.: 1 / Fragment: residues 132-146 / Source method: obtained synthetically / Source: (synth.) Borreliella burgdorferi B31 (bacteria) / References: UniProt: Q07337

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Antibody , 2 types, 2 molecules HL

#1: Antibody	Monoclonal 8C1 Fab Heavy Chain Mass: 23659.461 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	Monoclonal 8C1 Fab Light Chain Mass: 23965.961 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, 387 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#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.: 377 / 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: 2.36 Å³/Da / Density % sol: 47.93 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris- pH 7.0, 200 mM Li2SO4, and 2.0 M Ammonium sulfate

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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: May 31, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.64→50 Å / Num. obs: 56365 / % possible obs: 99.5 % / Redundancy: 19.3 % / B_iso Wilson estimate: 22.94 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.089 / R_pim(I) all: 0.021 / R_rim(I) all: 0.092 / Χ²: 0.908 / Net I/σ(I): 6.3 / Num. measured all: 1088903

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
1.64-1.67	11.7	1.041	2570	0.855	0.96	0.296	1.084	0.343	91.1
1.67-1.7	15.4	0.907	2805	0.948	0.986	0.225	0.935	0.355	100
1.7-1.73	18.5	0.875	2831	0.958	0.989	0.201	0.898	0.37	100
1.73-1.77	19.8	0.735	2789	0.968	0.992	0.165	0.753	0.375	100
1.77-1.81	20.5	0.59	2810	0.982	0.995	0.131	0.605	0.394	100
1.81-1.85	20.7	0.489	2827	0.987	0.997	0.108	0.501	0.416	100
1.85-1.89	20.8	0.418	2834	0.988	0.997	0.093	0.428	0.44	100
1.89-1.94	20.5	0.327	2831	0.992	0.998	0.073	0.335	0.48	100
1.94-2	20.5	0.256	2830	0.994	0.998	0.057	0.262	0.515	100
2-2.07	20.2	0.208	2789	0.996	0.999	0.047	0.213	0.555	100
2.07-2.14	19.8	0.173	2857	0.997	0.999	0.039	0.177	0.619	100
2.14-2.23	18.6	0.147	2831	0.997	0.999	0.035	0.151	0.683	100
2.23-2.33	18.6	0.132	2803	0.997	0.999	0.032	0.136	0.746	100
2.33-2.45	20	0.114	2828	0.998	1	0.026	0.117	0.81	100
2.45-2.6	21.4	0.1	2842	0.998	1	0.022	0.102	0.935	100
2.6-2.8	21.1	0.09	2840	0.999	1	0.02	0.092	1.199	100
2.8-3.09	20.7	0.077	2829	0.999	1	0.017	0.079	1.6	100
3.09-3.53	19.9	0.067	2852	0.999	1	0.015	0.069	2.207	100
3.53-4.45	17	0.058	2853	0.999	1	0.014	0.06	2.593	99.4
4.45-50	20	0.049	2914	0.999	1	0.011	0.05	2.263	99.8

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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: 1.64→46.09 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.2306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1887	2878	5.12 %
R_work	0.1605	53370	-
obs	0.162	56248	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→46.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3377	0	22	377	3776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0178	3524
X-RAY DIFFRACTION	f_angle_d	1.41	4800
X-RAY DIFFRACTION	f_chiral_restr	0.092	547
X-RAY DIFFRACTION	f_plane_restr	0.0122	610
X-RAY DIFFRACTION	f_dihedral_angle_d	6.4769	483

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 (%)
1.64-1.67	0.3124	115	0.2694	2410	X-RAY DIFFRACTION	93.41
1.67-1.69	0.2867	151	0.2379	2469	X-RAY DIFFRACTION	99.66
1.69-1.72	0.2633	144	0.2139	2540	X-RAY DIFFRACTION	99.96
1.72-1.76	0.2471	106	0.1946	2585	X-RAY DIFFRACTION	99.89
1.76-1.79	0.2025	126	0.176	2536	X-RAY DIFFRACTION	99.81
1.79-1.83	0.2029	145	0.1632	2552	X-RAY DIFFRACTION	99.81
1.83-1.88	0.2044	137	0.1719	2515	X-RAY DIFFRACTION	99.89
1.88-1.92	0.2048	164	0.1632	2521	X-RAY DIFFRACTION	100
1.92-1.97	0.193	126	0.1621	2579	X-RAY DIFFRACTION	99.96
1.97-2.03	0.1793	147	0.1618	2531	X-RAY DIFFRACTION	99.93
2.03-2.1	0.1763	115	0.1508	2580	X-RAY DIFFRACTION	100
2.1-2.17	0.1781	150	0.1469	2540	X-RAY DIFFRACTION	99.89
2.17-2.26	0.1568	138	0.1428	2516	X-RAY DIFFRACTION	99.96
2.26-2.36	0.1963	143	0.1557	2554	X-RAY DIFFRACTION	100
2.36-2.49	0.1785	138	0.1502	2543	X-RAY DIFFRACTION	99.96
2.49-2.64	0.1855	148	0.1545	2549	X-RAY DIFFRACTION	100
2.64-2.85	0.1517	133	0.1533	2579	X-RAY DIFFRACTION	99.93
2.85-3.13	0.1922	134	0.1627	2558	X-RAY DIFFRACTION	99.78
3.13-3.59	0.1887	134	0.1534	2557	X-RAY DIFFRACTION	99.78
3.59-4.51	0.1746	130	0.144	2559	X-RAY DIFFRACTION	99.12
4.52-46.09	0.1982	154	0.176	2597	X-RAY DIFFRACTION	98.92

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	2.00180155963	1.47112370074	-0.599274312118	3.69153332186	-4.31448475424	6.32089303448	0.0188694183625	0.453266894502	-0.284551577534	-0.296203309409	-0.04996826162	-0.240781023574	0.362619838435	0.251066151959	0.0842332953779	0.179760552478	0.0253092636443	-0.0119916122317	0.306223205102	-0.0694742489748	0.270124676289	7.77368591556	-41.3795611144	-13.8188964349
2	1.71230608337	0.644456235025	0.779101771807	5.21476390627	-2.2202991644	4.0740770783	0.137384540025	0.257838132293	-0.163089902699	0.226306875333	0.0420890350711	-0.0451330669329	-0.450721758857	0.130816333045	-0.064348053972	0.0912814237595	0.075647685909	0.00370869123669	0.278158399382	-0.0408240522798	0.212963071113	9.4983562882	-41.0705563331	-10.8716731134
3	2.38682426101	0.624485253371	0.341590398322	6.58854085129	-2.21090339631	3.96674294218	-0.0151860449363	0.582403689852	0.0733934275037	-0.741191615453	0.132773090336	0.346068647883	-0.016085432879	-0.0563598834575	-0.185657141329	0.239461220162	0.040259688259	0.00249943564619	0.422635892293	-0.0168192252293	0.239993613367	4.81125557835	-36.3072892222	-20.2575093092
4	2.23057450519	-1.88250583843	-2.06892814366	3.99370618639	2.57982489546	5.16192635713	-0.178302138672	-0.627023799059	0.185746762577	0.104890479663	0.201503131334	0.246737846523	-0.376958511088	-0.561486272521	0.036903678118	0.356671579364	0.0711727424287	0.00448783663188	0.451463987558	0.0333816112112	0.237468239858	16.429623804	-39.7216429311	37.1470683132
5	1.49234219119	1.42942464986	-0.0557770175898	3.22591536815	-3.44377566301	5.98025820329	0.01910966414	-0.186381259928	0.331104296267	0.165184062006	0.132799536389	0.268795161953	-0.412406508415	-0.254014998493	-0.315557277634	0.249580510156	0.0878646597747	0.0185865589709	0.182167565561	-0.0460894441441	0.204172676126	18.3262341266	-24.7906192508	15.8407263865
6	2.06722822064	1.53475629408	-3.29035782902	2.40876397663	-4.67674708199	9.26206621548	-0.15086932971	-0.00893055311402	0.0459192449866	0.255939598736	0.184315055437	-0.0365421509895	-0.560760584375	-0.667883320792	-0.169139622679	0.290493520353	0.103144821771	0.0201780203413	0.313006318918	-0.0443234497731	0.190729003054	15.220822672	-28.6678789491	28.4369625185
7	3.09016393193	-0.292651519141	2.29854183754	3.00053825692	-1.96712656738	2.73352095213	0.0216301791373	-0.0947740459266	0.10220377992	0.015099996657	-0.0498495941633	-0.119714716653	0.162239517852	0.177274766078	-0.0277545106438	0.127795555588	0.0275011483055	-0.00649157860845	0.15401959212	0.0032768869308	0.154796411124	24.9076278253	-34.7533332181	23.1364275015
8	3.45997475313	-1.38455617261	1.29543202559	5.27439264097	-0.344905500358	3.54658885717	-0.0550418976568	-0.219289314749	0.577728085669	0.466317801296	0.0485171518456	-0.489586404739	-0.860216542013	0.281041712067	-0.0486603778111	0.256079449998	0.0184804533591	-0.0376637015916	0.202807245969	-0.0105246009703	0.207859073067	28.0924722507	-28.3357238836	25.9889362799
9	7.78282406002	1.0996150148	-4.79111517266	1.92339037468	-1.09380632753	3.71015359163	0.0866034677845	-0.397571925022	0.237363883235	0.345028112558	-0.177967819107	-0.227720832286	-0.725297386565	0.481526366656	-0.0825280674073	0.243834218739	-0.0057866558515	-0.0255166585341	0.172492055874	0.00284276572927	0.19234096289	26.5005099956	-25.0789405069	17.5656793926
10	0.460829927035	-0.200257807046	0.518473850948	1.80960683528	-2.50766392884	4.64311272276	-0.0106862025277	-0.157333210322	0.0526935511049	0.197306523566	0.0120777159722	-0.00958020432078	-0.266241333199	0.0776563852647	-0.0500531977416	0.176498620702	0.0148931366568	0.00593225067419	0.200210757805	-0.0106914877685	0.178204121089	18.9800674221	-30.2035173214	14.1231690389
11	7.85320708047	5.29188678971	1.01052914656	6.78926011128	0.503762230987	1.17319436302	-0.340783091241	0.618639567532	0.269627773589	-0.385134631633	0.220419167181	0.45031167461	-0.0386836421686	0.048787723237	0.100240149596	0.172421227804	0.0116038224455	0.0235671397747	0.241294497937	-0.00479537364632	0.206981962605	2.56198603046	-29.0241846912	-7.77549587498
12	3.89468902061	0.859997903564	-0.346105949083	0.666726421314	-0.137503352417	1.26663325857	-0.0961170809852	0.0694733057034	-0.36034319661	-0.0405115807226	0.0556416304968	-0.0571504465604	0.0522765789716	-0.132135442206	0.0395114372768	0.169420952733	0.00976328937439	0.0342161814921	0.162580589499	0.0124971783835	0.213493465953	6.37100088705	-31.7990197202	-1.3409788158
13	8.30469162847	5.19682349051	2.93793587404	4.26186720621	2.02088946255	1.88029670261	-0.252169812574	-0.222139381395	0.134693984891	-0.245349586908	0.103976132119	0.151396197085	-0.219108053271	-0.205299682576	0.0828920872256	0.199868582079	0.0300269785307	0.0301311484934	0.223745788489	0.00317848635967	0.218976281539	-1.37683056529	-25.9399636213	0.346530456315
14	7.1891816342	3.1679446943	2.28377768009	6.36451801689	0.406934886633	4.98712653027	-0.219253857107	-0.296046045358	0.969714424948	-0.103811678871	-0.0755451388487	0.341859590839	-0.315660808691	-0.861821126702	0.248378772544	0.242842274577	0.071941510382	0.0136415376296	0.312771977159	0.00114348749006	0.32138022322	-1.34221411137	-21.9922539747	-2.8776880907
15	2.65349994588	0.0777294204866	2.13049256711	2.42930505482	0.753912304174	4.86826673909	0.0259957267553	0.0250660646973	-0.13456590962	-0.0771308642196	0.0215174778499	0.00656298368277	0.0596829027298	-0.0373850987655	-0.0482812525963	0.182518762442	0.0360374610361	-0.00453420521255	0.183634509306	0.0252621307363	0.218500977201	23.9827861659	-54.2083932665	18.7039559788
16	3.34124334883	0.628153749353	-1.34478951181	6.91993767957	-2.31546448808	7.58453150372	0.112817104129	0.0281341881169	0.0272009681998	-0.471513916396	0.160280487124	0.540563856469	-0.361963849907	-0.691043181376	-0.282305424658	0.158873332156	0.0404155757111	-0.0396784721129	0.170431982466	0.00112300525153	0.163073658061	14.8668146233	-45.5273392725	17.3191429985
17	4.021452446	-0.849603725377	1.27780060882	3.35035558291	1.03678884292	4.61374277291	0.0906019083695	-0.220425208249	-0.310451650513	-0.0417633936937	-0.0426149227375	0.501909718294	0.0384601146512	-0.62668766388	-0.052044083885	0.16131022327	-0.0255135866177	-0.0126183525759	0.246984721389	0.076744654797	0.247311566952	15.477661872	-55.5185108045	23.0402708094
18	1.62869847243	-0.412544369422	1.63680455097	0.293004094078	-0.559031664952	2.54460013369	0.0518641717773	0.0359224056875	-0.138940757662	0.00172989528501	0.0419289212222	0.0849815590519	0.00254936986491	-0.122863683731	-0.127227454421	0.132968680581	0.0282795523456	0.0141692928251	0.196049247748	-0.00462541064387	0.188073181381	12.361041963	-43.8432583932	4.33825103703

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 134 through 155 )	L	B	134 - 155	134 - 155
2	2	chain 'L' and (resid 156 through 177 )	L	B	156 - 177	156 - 177
3	3	chain 'L' and (resid 178 through 218 )	L	B	178 - 218	178 - 218
4	4	chain 'P' and (resid 132 through 145 )	P	C	132 - 145	1 - 14
5	5	chain 'H' and (resid 1 through 17 )	H	A	1 - 17	1 - 17
6	6	chain 'H' and (resid 18 through 32 )	H	A	18 - 32	18 - 32
7	7	chain 'H' and (resid 33 through 57 )	H	A	33 - 57	33 - 57
8	8	chain 'H' and (resid 58 through 76 )	H	A	58 - 76	58 - 76
9	9	chain 'H' and (resid 77 through 91 )	H	A	77 - 91	77 - 91
10	10	chain 'H' and (resid 92 through 120 )	H	A	92 - 120	92 - 120
11	11	chain 'H' and (resid 121 through 146 )	H	A	121 - 146	121 - 141
12	12	chain 'H' and (resid 147 through 189 )	H	A	147 - 189	142 - 184
13	13	chain 'H' and (resid 190 through 204 )	H	A	190 - 204	185 - 199
14	14	chain 'H' and (resid 205 through 215 )	H	A	205 - 215	200 - 210
15	15	chain 'L' and (resid 1 through 37 )	L	B	1 - 37	1 - 37
16	16	chain 'L' and (resid 38 through 53 )	L	B	38 - 53	38 - 53
17	17	chain 'L' and (resid 54 through 80 )	L	B	54 - 80	54 - 80
18	18	chain 'L' and (resid 81 through 133 )	L	B	81 - 133	81 - 133

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