PDB-9bx7: Fab 8C1 in complex with OspCA peptide P20 (residues 131-150)

ID or keywords:

Entry

Database: PDB / ID: 9bx7

Title

Fab 8C1 in complex with OspCA peptide P20 (residues 131-150)

Components

8C1 Fab Heavy Chain
8C1 Fab Light Chain
P20 peptide from Outer surface protein C

Keywords

IMMUNE SYSTEM/ANTIGEN / Human monoclonal Fab 8C1 in complex with Outer Surface Protein C type A P20 peptide (residues 131-150) / IMMUNE SYSTEM / IMMUNE SYSTEM-ANTIGEN complex

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 (Lyme disease spirochete)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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 P20 (residues 131-150)
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	May 22, 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	9bx7.cif.gz	318 KB	Display	PDBx/mmCIF format
PDB format	pdb9bx7.ent.gz	216.3 KB	Display	PDB format
PDBx/mmJSON format	9bx7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bx7_validation.pdf.gz	466.7 KB	Display	wwPDB validaton report
Full document	9bx7_full_validation.pdf.gz	471 KB	Display
Data in XML	9bx7_validation.xml.gz	25.8 KB	Display
Data in CIF	9bx7_validation.cif.gz	34.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/9bx7 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/9bx7	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: 8C1 Fab Heavy Chain

L: 8C1 Fab Light Chain

P: P20 peptide from Outer surface protein C

hetero molecules

50.4 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)	106.146, 106.146, 71.485
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
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: -x,-y,z+1/2

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide	P20 peptide from Outer surface protein C / pC / P23 Mass: 2266.526 Da / Num. of mol.: 1 / Fragment: residues 131-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete) Strain: B31 / Gene: ospC, BB_B19 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q07337

#3: Protein/peptide

P20 peptide from Outer surface protein C / pC / P23

Mass: 2266.526 Da / Num. of mol.: 1 / Fragment: residues 131-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Borreliella burgdorferi (Lyme disease spirochete)
Strain: B31 / Gene: ospC, BB_B19 / Production host:

Escherichia coli B (bacteria) / References: UniProt: Q07337

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Antibody , 2 types, 2 molecules HL

#1: Antibody	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	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 , 4 types, 339 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.33 Å³/Da / Density % sol: 47.21 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Tris- pH 7.0, 200 mM LiSO4, 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: Apr 12, 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: 1.7→50 Å / Num. obs: 50294 / % possible obs: 98.8 % / Redundancy: 20 % / B_iso Wilson estimate: 26.4 Å² / CC_1/2: 0.99 / Net I/σ(I): 35.9
Reflection shell	Resolution: 1.7→1.73 Å / Num. unique obs: 2431 / CC_1/2: 0.89

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→33.31 Å / SU ML: 0.2153 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.3874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1967	2469	4.97 %
R_work	0.1757	47169	-
obs	0.1768	49638	98.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.38 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→33.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3352	0	26	332	3710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0051	3492
X-RAY DIFFRACTION	f_angle_d	1.0913	4752
X-RAY DIFFRACTION	f_chiral_restr	0.0529	539
X-RAY DIFFRACTION	f_plane_restr	0.0074	602
X-RAY DIFFRACTION	f_dihedral_angle_d	6.1527	477

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 (%)
1.7-1.73	0.4066	122	0.3796	2578	X-RAY DIFFRACTION	97.16
1.73-1.77	0.3525	131	0.3165	2562	X-RAY DIFFRACTION	97.79
1.77-1.81	0.2686	142	0.2527	2601	X-RAY DIFFRACTION	98.1
1.81-1.85	0.2323	136	0.2196	2583	X-RAY DIFFRACTION	98.3
1.85-1.9	0.2179	148	0.2035	2605	X-RAY DIFFRACTION	98.25
1.9-1.95	0.2197	126	0.2046	2564	X-RAY DIFFRACTION	98.18
1.95-2.01	0.2157	138	0.189	2620	X-RAY DIFFRACTION	98.43
2.01-2.07	0.1968	137	0.1864	2613	X-RAY DIFFRACTION	98.71
2.07-2.14	0.2195	140	0.1922	2609	X-RAY DIFFRACTION	98.64
2.14-2.23	0.2038	138	0.1617	2598	X-RAY DIFFRACTION	98.45
2.23-2.33	0.2367	161	0.1759	2610	X-RAY DIFFRACTION	99.18
2.33-2.45	0.1722	128	0.1705	2637	X-RAY DIFFRACTION	99.18
2.45-2.61	0.2083	143	0.1766	2630	X-RAY DIFFRACTION	99.39
2.61-2.81	0.2082	113	0.1704	2661	X-RAY DIFFRACTION	99.39
2.81-3.09	0.1939	145	0.1745	2647	X-RAY DIFFRACTION	99.57
3.09-3.54	0.1867	158	0.154	2655	X-RAY DIFFRACTION	99.65
3.54-4.46	0.1578	161	0.144	2646	X-RAY DIFFRACTION	99.72
4.46-33.31	0.1865	102	0.1784	2750	X-RAY DIFFRACTION	99.51

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	1.76766276686	0.965948746452	-1.98320913961	1.80103440432	-2.95498577561	7.11972362178	-0.0546009857439	-0.179946812351	0.1788640297	0.137723253813	0.123697756261	0.140583911021	-0.272736135539	-0.387034720782	-0.127968768392	0.253895466569	0.0655250645605	0.0279250588211	0.253142915199	-0.0523609274184	0.236298266929	16.7002579501	-26.4999293468	22.0091753844
2	3.67825145492	0.369021595202	2.19137948472	3.39606245984	-1.69420729715	2.39909764773	0.0545444962774	-0.125971102155	0.0270213408018	0.041293230003	-0.0425328763199	-0.111930790421	0.170863550592	0.165076383557	-0.0586784078357	0.142843870356	0.0371814161116	-0.000421260713235	0.165229064497	-0.000277976479071	0.16058837138	24.9133429905	-34.6561775113	22.5919172213
3	4.25443242968	-1.80505011938	0.227672941693	5.84604248737	0.135214474558	4.63045087434	0.0370273953056	-0.501156667409	0.418452124922	0.226840466275	0.0167318233142	-0.287583691193	-0.49221878148	0.317867399801	-0.0816930501988	0.206919130785	-0.0273827303515	-0.0479160686165	0.20078936072	-0.0365146681277	0.232442222139	28.145771564	-28.161426557	25.9409062225
4	0.688214706091	-0.0288770383518	0.587967406396	1.61673005885	-1.36975054176	3.40781191029	-0.0338467010194	-0.131357727947	0.12820332792	0.0970861505126	0.00134398903778	-0.0712066827738	-0.147589604692	0.0650781854313	0.0754945261595	0.149318908585	0.0228618203722	0.0191713506471	0.156587925493	-0.0105074346733	0.19042409033	21.3245661705	-28.5650702118	15.6260792559
5	3.67738124924	2.36331060243	0.634855210396	3.29758286754	0.543526057456	1.57569977296	-0.298730708802	0.741421736542	0.321594191498	-0.262741046538	0.224852829732	0.38529328405	-0.0459507347342	-0.0138527611749	0.0929094033427	0.146099657912	-0.00417615168099	0.020157751588	0.286296383822	0.0112814293733	0.239465077213	2.58593632797	-29.0179196554	-8.02596899741
6	7.09207643763	2.04649237124	-0.611519311143	1.23889732367	0.212738464928	1.71102671033	-0.0740717742363	0.0508777182287	-0.145254123304	-0.0415860241879	0.016154010594	0.011030770722	0.0150416023135	-0.220644705946	0.0641613161166	0.162951717024	0.02891102181	0.0294814078715	0.153348669403	0.0440501087972	0.204258809895	4.50327218715	-30.0076350079	-0.825209977636
7	8.62354859202	5.28206984471	4.3678032058	7.19565836701	3.24870094251	7.49390279863	-0.508826982194	0.292437904956	0.731672053812	-0.207329867863	0.142852118946	0.196227157948	-0.514618778056	-0.559669989232	0.27508156956	0.246125012657	0.0956022217094	0.0356884644162	0.325330251209	0.041047688227	0.372481170697	-1.00086574211	-21.9644345072	-2.91242529972
8	3.33476536722	-0.624659178461	1.2813026753	2.56471949877	0.323053152076	4.01690631625	0.109193066634	-0.0511791456961	-0.353735799237	-0.117005067227	0.0276737337525	0.0554993785537	0.205059383683	-0.135533560071	-0.0997842399241	0.168952767007	-0.021992321029	-0.0139316936706	0.135560453414	0.0333334329038	0.215043039882	20.8533661631	-51.090452798	18.3395769472
9	4.57920200461	-0.579205013634	1.36212594786	3.24353920989	0.460077804055	5.12438294548	0.124034903833	-0.330141645434	-0.335434619467	0.0509494731177	-0.0275511926418	0.336317344933	0.0906060983498	-0.642328566394	-0.101212525656	0.22830340379	-0.0567736101739	-0.0195385620929	0.269001471067	0.0756509904337	0.301057928592	15.3524327025	-55.2393979527	23.1458133089
10	2.19732191546	-0.196566094413	1.88391022541	0.223719179466	-0.579090108508	2.94280272919	0.0488052467501	0.0931917911916	-0.159015412673	0.0435483721516	0.0457060189505	0.0484790127011	-0.0380125477532	-0.178647621602	-0.158235421778	0.144625560594	0.0473497917474	0.0155425258699	0.214365770623	-0.0267470068403	0.208548275792	12.3108368431	-43.7469860943	4.35149049111
11	3.36232550436	0.597796894084	0.247379942283	5.20258565002	-1.4559264892	3.21107348234	-0.0804294778512	0.956198824631	-0.188971487236	-0.524478382963	0.207039380143	0.00482670281455	0.0364091635227	0.0188410149497	-0.115509675816	0.176331080022	-0.00772163596271	0.0229740037884	0.517752647224	-0.0974414950637	0.253184855509	7.07725633411	-39.1244129749	-16.0786002591
12	6.74829254546	-3.79726457835	-3.94211971784	6.54022455565	3.23064443697	9.72772188416	-0.571350417846	-0.867406980106	-0.208833608306	0.804386923562	0.424753060566	0.495255425579	0.466130749851	-0.626105315609	0.0895995112999	0.406284899042	0.0252616287608	0.0334893519327	0.488052043937	0.0611811663987	0.281562592817	17.9645754076	-40.4287783021	37.4890000544

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 'H' and (resid 1 through 32 )	H	A	1 - 32	1 - 32
2	2	chain 'H' and (resid 33 through 57 )	H	A	33 - 57	33 - 57
3	3	chain 'H' and (resid 58 through 76 )	H	A	58 - 76	58 - 76
4	4	chain 'H' and (resid 77 through 120 )	H	A	77 - 120	77 - 120
5	5	chain 'H' and (resid 121 through 146 )	H	A	121 - 146	121 - 141
6	6	chain 'H' and (resid 147 through 204 )	H	A	147 - 204	142 - 199
7	7	chain 'H' and (resid 205 through 215 )	H	A	205 - 215	200 - 210
8	8	chain 'L' and (resid 1 through 53 )	L	B	1 - 53	1 - 53
9	9	chain 'L' and (resid 54 through 80 )	L	B	54 - 80	54 - 80
10	10	chain 'L' and (resid 81 through 133 )	L	B	81 - 133	81 - 133
11	11	chain 'L' and (resid 134 through 216 )	L	B	134 - 216	134 - 216
12	12	chain 'P' and (resid 134 through 146 )	P	C	134 - 146	1 - 13

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Antibody , 2 types, 2 molecules HL

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Non-polymers , 4 types, 339 molecules

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