PDB-8shv: 38B7 unliganded

ID or keywords:

Entry

Database: PDB / ID: 8shv

Title

38B7 unliganded

Components

38B7 heavy chain
38B7 light chain

Keywords

IMMUNE SYSTEM / allergy / peanut / antibody

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

Spiller, B.W. / Shrem, R.A.

Funding support

United States, 1items

Citation

Journal: J.Allergy Clin.Immunol. / Year: 2025
Title: Structural determinants of peanut induced anaphylaxis.
Authors: Smith, S.A. / Shrem, R.A. / Lanca, B.B.C. / Zhang, J. / Wong, J.J.W. / Croote, D. / Peebles Jr., R.S. / Spiller, B.W.

History

Deposition	Apr 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8shv.cif.gz	319.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8shv.ent.gz	216.9 KB	Display	PDB format
PDBx/mmJSON format	8shv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sh/8shv ftp://data.pdbj.org/pub/pdb/validation_reports/sh/8shv	HTTPS FTP

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Related structure data

Related structure data	8shwC 8si1C 8sj4C 8sj6C 8sjaC C: citing same article (ref.)

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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

L: 38B7 light chain

H: 38B7 heavy chain

hetero molecules

47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, The Fab binds a CH1 resin

Unit cell

Length a, b, c (Å)	61.980, 65.810, 136.670
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Antibody	38B7 light chain Mass: 23771.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)
#2: Antibody	38B7 heavy chain Mass: 23708.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O
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: 2.84 Å³/Da / Density meas: 0.567 Mg/m³ / Density % sol: 58.1 % / Description: plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 4000, 100 mM MES pH 6.5 / PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.12713 Å / Relative weight: 1
Reflection	Resolution: 1.58→50 Å / Num. obs: 77127 / % possible obs: 99.8 % / Redundancy: 7.4 % / B_iso Wilson estimate: 25.33 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.58→1.61 Å / Redundancy: 6.1 % / R_merge(I) obs: 1.406 / Num. unique obs: 3660 / CC_1/2: 0.406 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2	0.5.900-ga3de5862-dials-1.14	data reduction
DIALS	1.14.12-g6954cb231-release	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.58→30.22 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1784	3735	4.85 %
R_work	0.1641	73304	-
obs	0.1648	77039	99.65 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.58→30.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3309	0	15	489	3813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0132	3446
X-RAY DIFFRACTION	f_angle_d	1.1312	4698
X-RAY DIFFRACTION	f_chiral_restr	0.0763	520
X-RAY DIFFRACTION	f_plane_restr	0.0095	606
X-RAY DIFFRACTION	f_dihedral_angle_d	6.742	495

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 (%)
1.58-1.6	0.3384	136	0.3248	2545	X-RAY DIFFRACTION	95.55
1.6-1.62	0.2949	137	0.2878	2650	X-RAY DIFFRACTION	98.9
1.62-1.64	0.282	133	0.2664	2714	X-RAY DIFFRACTION	100
1.64-1.67	0.2945	137	0.2482	2690	X-RAY DIFFRACTION	99.93
1.67-1.69	0.2584	132	0.2382	2683	X-RAY DIFFRACTION	100
1.69-1.72	0.2847	119	0.2135	2683	X-RAY DIFFRACTION	99.93
1.72-1.75	0.2706	139	0.2081	2706	X-RAY DIFFRACTION	99.79
1.75-1.78	0.2452	130	0.2045	2730	X-RAY DIFFRACTION	99.97
1.78-1.81	0.2425	147	0.1996	2667	X-RAY DIFFRACTION	100
1.81-1.84	0.2353	124	0.1853	2713	X-RAY DIFFRACTION	99.89
1.84-1.88	0.201	112	0.1724	2744	X-RAY DIFFRACTION	99.96
1.88-1.92	0.1842	121	0.1664	2716	X-RAY DIFFRACTION	99.79
1.92-1.97	0.1852	162	0.1642	2637	X-RAY DIFFRACTION	99.96
1.97-2.02	0.1644	163	0.1606	2698	X-RAY DIFFRACTION	99.93
2.02-2.07	0.2121	162	0.159	2683	X-RAY DIFFRACTION	99.86
2.07-2.13	0.1802	147	0.1568	2688	X-RAY DIFFRACTION	99.3
2.13-2.2	0.1867	121	0.1564	2736	X-RAY DIFFRACTION	99.48
2.2-2.28	0.1863	139	0.1552	2699	X-RAY DIFFRACTION	99.89
2.28-2.37	0.1635	131	0.1562	2715	X-RAY DIFFRACTION	99.96
2.37-2.48	0.1722	138	0.1541	2732	X-RAY DIFFRACTION	99.86
2.48-2.61	0.1716	151	0.1637	2712	X-RAY DIFFRACTION	99.97
2.61-2.77	0.1932	151	0.16	2719	X-RAY DIFFRACTION	99.9
2.77-2.99	0.1615	118	0.163	2790	X-RAY DIFFRACTION	99.9
2.99-3.29	0.1782	155	0.157	2748	X-RAY DIFFRACTION	99.79
3.29-3.76	0.163	129	0.1529	2777	X-RAY DIFFRACTION	99.93
3.76-4.73	0.135	149	0.132	2812	X-RAY DIFFRACTION	99.56
4.73-30.22	0.171	152	0.1786	2917	X-RAY DIFFRACTION	99.38

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	8.12122295032	4.16776306489	4.56191766288	7.75185779445	5.15150487442	6.25657428498	0.0167475594682	-0.0187746990669	-0.26135804584	0.331662619524	0.204856568231	-0.263049459385	0.331390986609	-0.0271639859506	-0.272405542071	0.27467325561	0.0583982055985	-0.019839534591	0.257473401104	0.0262389418179	0.181150643465	32.025776166	48.951263882	94.6626639237
2	3.12337883482	0.296316829198	0.592771500118	3.78943707943	0.0302296287143	3.40533930307	-0.0122144870716	0.107550444695	-0.124793783682	-0.0503982539728	0.0481365854541	-0.325713523119	0.0641156119404	0.099209406288	-0.039901671081	0.202540939875	0.0297479947571	0.0193694382646	0.232189396478	-0.0129766586647	0.187525805099	36.3205120467	51.4372904393	84.9400753863
3	4.05676447161	0.3277385302	1.92722808828	2.84558534474	2.03423853912	4.70836121979	-0.0652171787569	-0.0809858056699	0.125103211208	-0.144449254318	0.0874394433509	-0.166195933954	-0.219340421895	0.000380974745583	0.0266712534043	0.214420343086	0.0339549296833	0.0115288476667	0.164384016939	0.019927072789	0.169464859592	32.6254229597	55.3330210215	88.8573960861
4	3.2151003912	-0.272879904771	0.570233633425	3.44492858019	4.01443313717	5.7792768565	-0.0805806713683	0.0885460568558	-0.132959258355	-0.187031627015	-0.147758722855	0.193886515104	-0.231012858424	-0.343754915091	0.338478583756	0.243704357915	0.00383934921667	0.0241275135925	0.162786496723	0.0241653458622	0.185098112306	26.6194198232	48.3135374265	84.188305793
5	3.13527220249	0.306339909377	-0.388555289394	0.879328543436	0.0576504195139	1.37131358137	0.0460071311584	0.0699203927348	-0.0941061595498	0.0664657291807	-0.0301706360495	0.119210083918	0.0499364428439	-0.0212336815394	0.0320703758884	0.218261846121	-0.00802230676356	0.00685944957133	0.175623071041	-0.046460475781	0.196368279257	8.96419784462	64.9279862563	108.427579299
6	8.89331477757	3.49383305193	-3.32411024664	2.11991911511	-2.44907249636	2.97910967641	-0.00178973194057	-0.122529813413	0.0447743126896	0.0135884902469	0.0994684748418	0.103487258912	0.0835749340923	0.0190273802201	0.0100605391852	0.263662173899	-0.0135650857711	0.0153704988706	0.17101757576	-0.0439806908719	0.239367874464	3.06381437635	57.0505996289	106.508414496
7	8.29172947503	-0.163853063557	-1.14106751327	0.882054833065	-0.0849726461222	1.49494561768	0.0023710218308	-0.276776022273	-0.0561727382958	0.116916150761	-0.0042907268269	0.0671603752102	0.0855688844103	-0.0103722327164	-0.00243426011329	0.22557699902	-0.0113298400201	0.0127051650025	0.116140462092	-0.051515871596	0.189765663083	6.72329006626	63.5784120287	110.573678373
8	2.42723878992	1.50658986119	-1.70899586712	1.51986419672	-0.544950172671	1.93630558151	0.0961812649785	0.368475446663	0.448682418322	-0.136985874087	-0.113955522253	0.0992428090812	-0.255793897375	-0.174573943409	-0.0684747133223	0.331718605609	0.0861120242965	-0.0494619250185	0.286230792969	-0.0230758499283	0.327271587881	15.0976644923	63.72093198	72.7045865971
9	4.3814450202	-0.0708564711422	-1.04599196737	2.37510277214	-0.836195110421	4.68244033485	-0.00717861294329	0.321094537901	0.0540126491248	-0.233218184634	-0.0858364286935	-0.03397751538	-0.0425745463496	0.13577283731	0.124815957461	0.199819134454	0.038442486548	-0.0345763617519	0.251595626356	-0.0199511321022	0.143861597139	23.1272618657	54.9025600071	69.9845618199
10	4.89410540403	4.69597692225	-4.29181179268	5.16000134972	-4.62669307157	4.19729449755	0.0250409496398	0.519812397432	0.181248580235	-0.480538143288	0.0457319038884	0.399319092228	0.156805262288	-0.178689213127	-0.0779958451006	0.318823893005	0.026347013889	-0.0484258206633	0.343988958463	-0.0316550755952	0.220045273371	16.9852943549	53.0081760851	66.4535597924
11	1.35413257831	-0.599299317602	-0.791165524369	1.04071161703	0.71223033011	1.77765581456	0.00597328241198	0.179569955405	0.0206553699305	-0.155998664305	-0.10799121562	0.0509192772706	-0.0152761177199	-0.151090293102	0.117451585026	0.235532300207	0.0129664349606	-0.0352219971588	0.246264476578	-0.0181538282285	0.172127865404	17.602232795	58.4097030441	75.3640070306
12	5.42333468745	0.346562809768	-1.7844174923	4.68499988331	-0.350517135152	0.599324743131	0.142337866253	-0.899018103205	-0.0827284514806	0.516694792152	-0.120644671941	0.048504369447	0.486223582676	-0.229170439145	0.000789707498481	0.235850450209	0.0428347283175	0.0255935894398	0.248637851401	0.00272246897557	0.201797135108	4.2622730486	76.1223559103	108.996825635
13	1.66003547228	0.211074453268	0.810636316346	2.24276658572	0.920942526727	3.1060102705	0.0216529571401	0.0337794884633	0.0214642068285	-0.0279205980306	-0.0907860739415	0.0521959455216	-0.15177245	-0.0413364718578	0.106217760806	0.168012252414	0.0142406704768	0.00864965958423	0.16528976026	-0.00694420904108	0.195570001647	7.9420222333	76.5019513577	98.818897334

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 1 through 24 )	L	A	1 - 24	1 - 24
2	2	chain 'L' and (resid 25 through 75 )	L	A	25 - 75	25 - 75
3	3	chain 'L' and (resid 76 through 92 )	L	A	76 - 92	76 - 92
4	4	chain 'L' and (resid 93 through 107 )	L	A	93 - 107	93 - 107
5	5	chain 'L' and (resid 108 through 151 )	L	A	108 - 151	108 - 151
6	6	chain 'L' and (resid 152 through 164 )	L	A	152 - 164	152 - 164
7	7	chain 'L' and (resid 165 through 214 )	L	A	165 - 214	165 - 214
8	8	chain 'H' and (resid 1 through 17 )	H	C	1 - 17	1 - 17
9	9	chain 'H' and (resid 18 through 60 )	H	C	18 - 60	18 - 60
10	10	chain 'H' and (resid 61 through 76 )	H	C	61 - 76	61 - 76
11	11	chain 'H' and (resid 77 through 124 )	H	C	77 - 124	77 - 124
12	12	chain 'H' and (resid 125 through 139 )	H	C	125 - 139	125 - 136
13	13	chain 'H' and (resid 140 through 220 )	H	C	140 - 220	137 - 217

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