PDB-9b88: Anti-OspC Fab 8C1

ID or keywords:

Entry

Database: PDB / ID: 9b88

Title

Anti-OspC Fab 8C1

Components

Heavy Chain of monoclonal 8C1 Fab
Light Chain of monoclonal 8C1 Fab

Keywords

IMMUNE SYSTEM / Antibody

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structure of anti-OspC Fab 8C1.
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	Mar 29, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9b88.cif.gz	315.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9b88.ent.gz	216.1 KB	Display	PDB format
PDBx/mmJSON format	9b88.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9b88_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	9b88_full_validation.pdf.gz	460.6 KB	Display
Data in XML	9b88_validation.xml.gz	27.2 KB	Display
Data in CIF	9b88_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/9b88 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/9b88	HTTPS FTP

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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)

Deposited unit

A: Heavy Chain of monoclonal 8C1 Fab

B: Light Chain of monoclonal 8C1 Fab

hetero molecules

48.3 kDa, 2 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)	105.962, 105.962, 70.775
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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Antibody , 2 types, 2 molecules AB

#1: Antibody	Heavy Chain of monoclonal 8C1 Fab 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	Light Chain of monoclonal 8C1 Fab Mass: 23965.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Light Chain of monoclonal / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 510 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.41 Å³/Da / Density % sol: 48.93 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM tri-sodium citrate pH 3.5 and 2.4 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 EIGER X 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: 1.73→50 Å / Num. obs: 54544 / % possible obs: 99 % / Redundancy: 19.4 % / B_iso Wilson estimate: 22.9 Å² / CC_1/2: 0.99 / Net I/σ(I): 44.4
Reflection shell	Resolution: 1.73→1.76 Å / Num. unique obs: 2666 / CC_1/2: 0.83

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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: 1.73→45.88 Å / SU ML: 0.1749 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.5121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1759	2432	5.15 %
R_work	0.1512	44801	-
obs	0.1525	47233	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→45.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3291	0	35	501	3827

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0126	3421
X-RAY DIFFRACTION	f_angle_d	1.1259	4652
X-RAY DIFFRACTION	f_chiral_restr	0.0715	527
X-RAY DIFFRACTION	f_plane_restr	0.0086	588
X-RAY DIFFRACTION	f_dihedral_angle_d	6.3233	469

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 (%)
1.73-1.77	0.2414	136	0.217	2642	X-RAY DIFFRACTION	100
1.77-1.8	0.2257	132	0.1895	2622	X-RAY DIFFRACTION	100
1.8-1.85	0.2251	153	0.176	2605	X-RAY DIFFRACTION	99.93
1.85-1.89	0.2108	146	0.1566	2631	X-RAY DIFFRACTION	100
1.89-1.94	0.182	149	0.1453	2597	X-RAY DIFFRACTION	100
1.94-2	0.1813	147	0.1463	2632	X-RAY DIFFRACTION	100
2-2.06	0.1823	131	0.1492	2629	X-RAY DIFFRACTION	100
2.06-2.14	0.1725	129	0.1569	2635	X-RAY DIFFRACTION	100
2.14-2.22	0.2007	157	0.1364	2611	X-RAY DIFFRACTION	100
2.22-2.33	0.1797	145	0.1463	2651	X-RAY DIFFRACTION	100
2.33-2.45	0.1813	147	0.1468	2622	X-RAY DIFFRACTION	100
2.45-2.6	0.178	152	0.1562	2627	X-RAY DIFFRACTION	100
2.6-2.8	0.176	145	0.1524	2621	X-RAY DIFFRACTION	100
2.8-3.08	0.1769	133	0.1585	2662	X-RAY DIFFRACTION	100
3.08-3.53	0.1515	142	0.1428	2662	X-RAY DIFFRACTION	100
3.53-4.45	0.1555	133	0.1286	2663	X-RAY DIFFRACTION	100
4.45-45.88	0.1748	155	0.167	2689	X-RAY DIFFRACTION	99.75

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	1.56388230946	-0.709776046591	-0.924593385481	2.32160044518	2.05159619883	4.89194040747	0.00566042270954	-0.0871570609948	0.0959781855617	-0.0527318600607	0.112314457895	-0.117740172422	-0.189360546757	0.297169290388	-0.154981524712	0.169469172066	-0.0142405721015	0.0216101868195	0.123021694758	0.0268580141953	0.174551189739	34.8696000334	67.2243605541	33.6809151849
2	3.73377061072	-1.67812361696	-3.15414031965	3.27903761985	3.21757675145	6.75359695738	0.0233110374077	0.294422921828	0.201411945406	-0.302970745824	-0.0127675052477	-0.049241249907	-0.165633770077	0.056898216339	-0.121166056192	0.228804900607	0.00183469314635	0.0342212410168	0.216413014092	0.0590410366447	0.178492396317	37.3332650114	63.7356241532	21.4294989124
3	2.81677424932	0.225186963264	0.909978079845	2.78592124629	1.11250043012	3.88323138152	0.112143120129	0.00441516667402	-0.0288603131573	0.0480072680741	0.0210913794797	0.100069034808	0.235049441091	-0.145842481977	-0.0643657535527	0.127992225074	0.00900075339483	-8.08967277488E-6	0.122132305291	0.00908668165248	0.147832634486	27.8462767317	56.5508396125	29.0743169787
4	4.459637789	0.904411393443	-1.39199681636	2.95086198179	-0.171865812104	3.46485358212	-0.0338016800661	0.654410802979	0.0731887495046	-0.336423274484	-0.0178231490357	0.0674095030152	-0.166845249246	-0.598423984871	0.00505810091603	0.20964682748	0.0362603081173	-0.0340624307784	0.203650849132	0.0145672130152	0.166893227467	23.1928788673	59.8452131008	21.6082073409
5	2.75632229353	1.80668786305	-3.63999124124	4.85970593205	-1.26891961514	6.01571556177	0.0716282849769	0.608769857781	0.524232409176	-0.234881319262	0.0638218264883	0.134982352876	-0.290474729403	-0.322194091339	-0.178549924996	0.198093579185	0.0331470487922	-0.0155638742298	0.198855737251	0.0559202316174	0.236793040969	28.5983747892	67.3986876905	23.9846535697
6	0.671531290636	0.175279851923	0.517974623366	1.58433035943	0.956696606893	2.33910121737	-0.00586420386166	0.0156767944255	0.0806128227829	0.00377183654538	0.0352693318681	0.0311421077341	-0.0506797278341	-0.0614834328244	-0.0308915234752	0.152195554982	-0.00189465064385	0.0125782984719	0.138064126589	0.0138493895691	0.169233680031	31.6629057494	62.5306766956	36.1505454174
7	1.66355562975	0.0768618214541	-1.14953888021	3.32995276248	2.09663803702	2.25661757764	-0.383726041307	-0.838673175071	-0.75990829985	1.09029108182	0.410014719317	-0.0972545524924	0.153956261938	0.784833928586	-0.108733297007	0.273844293266	0.0941144792049	-0.0304809642745	0.429139018931	0.0650505076438	0.338994447251	54.7124546577	60.3270264238	61.8889776749
8	2.84881146021	-0.481604331645	-0.00491655185609	0.724309073069	-0.553160744122	2.25160437003	-0.0951271261687	-0.0931145331887	-0.210906166079	0.0631711266535	0.0384563482882	0.0712139367815	0.0154147471085	0.249794739265	0.0440218197291	0.133943465354	0.00040929080941	0.0271555970894	0.154301610708	-0.00880407719898	0.189666144751	46.6773233228	60.5978646518	52.4214021274
9	5.9604242618	-2.29517849029	0.340753849482	2.0902344948	-0.443181026766	1.68006877328	-0.16209030005	0.0436276901765	0.0493048844597	0.226201079903	0.0430257934141	-0.117812345137	-0.175424004939	0.400965072041	0.0640598702021	0.11340529866	-0.0514410035858	0.0235929689174	0.225696666661	-0.0025079383256	0.136214205649	53.3287691432	66.0466549386	49.4335010372
10	2.5254017204	-3.82993364622	3.48963224225	7.11412867986	-3.75850833353	7.31315607607	-0.40880060749	-0.127621757183	0.423699901431	0.341202347782	0.133127300337	-0.184477846177	-0.661629772122	0.706226611954	0.244478184278	0.20918293231	-0.0629323704776	0.0207324364875	0.324630780244	0.00124392140231	0.24167179519	53.939529919	69.7050199939	52.9262701464
11	2.67230848983	0.266493591027	0.675983421502	2.40268801294	0.0173150439349	3.8473131105	-0.0176240093012	-0.00122822918543	-0.20015433389	0.183335245535	0.0817543045474	-0.080009928476	0.221241165991	0.119936300515	-0.030595947075	0.178000085783	0.0155457473598	-0.0146886697285	0.120327810739	-0.0159598635669	0.185825615256	29.5408327351	37.8242804173	31.178030095
12	2.52080520276	0.474034132315	-0.535248910601	5.0640678234	1.67986740101	5.79424849478	0.178115775134	-0.129975286056	-0.0240258116736	0.347146640241	0.0320985218207	-0.493940462231	-0.0809193335418	0.521802681785	-0.217188526952	0.162439751922	-0.00348836828014	-0.0237807704221	0.192183884247	-0.0122325317497	0.193335750964	38.3435677307	46.8352445949	32.5859197542
13	3.09737988851	0.623129082164	0.345902109857	2.84693439585	-0.230729635339	3.61967793726	0.0308606637835	0.131712046979	-0.194349476541	0.0337868343328	0.0979607758815	-0.427038964739	0.0841375385351	0.492604737489	-0.102214292419	0.184401823965	0.0575621513017	-0.0214629030754	0.240941198091	-0.0796376248072	0.240362568645	38.0596220832	36.8578527609	26.8866739758
14	2.14111815823	0.331482980425	0.0297367799634	2.76513103986	0.198122453617	3.33087335221	0.00613832064516	0.020671392288	-0.157390162938	0.106687934974	0.0752312741395	-0.206693605543	-0.00246198802682	0.410639271642	-0.0336992332613	0.149705546939	-0.0068151505151	-0.00885664551349	0.153646964328	-0.0237552630382	0.154841952392	33.8392776904	43.399368575	32.6295107264
15	1.45578288044	0.357341098249	2.18816215492	1.08788445061	0.752505646393	3.63426601227	0.435624117971	0.0349824816031	-0.297195889881	0.0281169500644	-0.032739637764	-0.211801528534	0.561036840163	0.170033201261	-0.418376936454	0.215992160764	0.0206674735129	-0.0274763508358	0.268977498064	0.0049296305107	0.266515353005	46.5247608937	43.0645237741	54.7467972673
16	4.50399851651	-1.09303825329	1.66136200958	2.51209608821	0.0465268025582	6.70117560919	-0.191281560803	0.0183995502141	0.781877958854	-0.196731353282	-0.111717164144	-0.512376559314	-1.66400614234	0.215488179471	0.243326916898	0.518382647286	-0.0525529919944	-0.0664690081452	0.275542908634	-0.0435832605793	0.284948816338	48.7431409957	70.6068012686	65.5514867093
17	1.39135550493	-0.0167023951611	0.87608506106	4.54043654045	3.12685050053	4.05309221447	0.206288724544	-0.293156638853	-0.208061620759	0.188152438592	0.00502322257203	-0.0673414091867	0.420911324986	-0.136109907446	-0.141640646861	0.190703153991	-0.0325059859752	-0.0239306521366	0.312437706838	0.0878132087726	0.257949480159	44.7367996927	49.5750322355	63.764119522
18	1.61185131331	1.07141799679	1.42179256304	2.01603310503	1.60483950365	4.6856061742	0.272227571751	-0.677186968986	-0.153018355538	0.317276495746	-0.0708779116659	-0.0271067127423	-0.0274676728413	-0.299763636319	-0.0783766725733	0.213478501283	-0.0584184617194	-0.00025374411056	0.474792721132	0.0509865035027	0.265475184532	39.6309067845	55.0968445974	70.2106683626
19	2.14762364166	-0.575542139832	0.568574689166	5.56359899446	4.53424293635	6.2545341561	0.132161253082	0.0204601979381	-0.0445944476476	-0.243440912119	0.303361877439	-0.250744772436	-0.0542718979892	0.517026854866	-0.2792142918	0.174433799463	-0.0309205055086	0.0147117920958	0.266603503867	0.0251093080157	0.210011901637	45.2806726616	49.8656693408	55.1077784579
20	2.39674299482	0.74989234423	1.12757623872	4.29416758916	1.50121398642	4.08318892994	0.319764464861	-0.514099650962	-0.0588146424067	0.696646036591	-0.203726130047	-0.502279199223	0.0785392571697	-0.00662286952605	-0.126780059114	0.221428998096	-0.0884419800468	-0.00881753562739	0.436096237471	0.0615688300668	0.242330301381	48.8151467898	55.6789180663	72.7169097629

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 'A' and (resid 1 through 17 )	A	A	1 - 17	1 - 17
2	2	chain 'A' and (resid 18 through 32 )	A	A	18 - 32	18 - 32
3	3	chain 'A' and (resid 33 through 52 )	A	A	33 - 52	33 - 52
4	4	chain 'A' and (resid 53 through 64 )	A	A	53 - 64	53 - 64
5	5	chain 'A' and (resid 65 through 83 )	A	A	65 - 83	65 - 83
6	6	chain 'A' and (resid 84 through 120 )	A	A	84 - 120	84 - 120
7	7	chain 'A' and (resid 121 through 135 )	A	A	121 - 135	121 - 134
8	8	chain 'A' and (resid 136 through 189 )	A	A	136 - 189	135 - 188
9	9	chain 'A' and (resid 190 through 204 )	A	A	190 - 204	189 - 203
10	10	chain 'A' and (resid 205 through 215 )	A	A	205 - 215	204 - 214
11	11	chain 'B' and (resid 1 through 37 )	B	B	1 - 37	1 - 37
12	12	chain 'B' and (resid 38 through 53 )	B	B	38 - 53	38 - 53
13	13	chain 'B' and (resid 54 through 80 )	B	B	54 - 80	54 - 80
14	14	chain 'B' and (resid 81 through 106 )	B	B	81 - 106	81 - 106
15	15	chain 'B' and (resid 107 through 123 )	B	B	107 - 123	107 - 123
16	16	chain 'B' and (resid 124 through 134 )	B	B	124 - 134	124 - 134
17	17	chain 'B' and (resid 135 through 155 )	B	B	135 - 155	135 - 155
18	18	chain 'B' and (resid 156 through 168 )	B	B	156 - 168	156 - 168
19	19	chain 'B' and (resid 169 through 186 )	B	B	169 - 186	169 - 186
20	20	chain 'B' and (resid 187 through 219 )	B	B	187 - 219	187 - 219

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Antibody , 2 types, 2 molecules AB

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Non-polymers , 4 types, 510 molecules

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Movie

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This page

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Open data

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Basic information

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Validation report

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Assembly

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Components

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Antibody , 2 types, 2 molecules AB

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Non-polymers , 4 types, 510 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi