PDB-6tcr: Crystal structure of the omalizumab Fab Ser81Arg, Gln83Arg and Le...

ID or keywords:

Entry

Database: PDB / ID: 6tcr

Title

Crystal structure of the omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

Components

(Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant) x 2

Keywords

IMMUNE SYSTEM /

Fab /

Antibody /

immunoglobulin

Function / homology

DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Mitropoulou, A.N. / Ceska, T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.

Funding support

United Kingdom, 2items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization.
Authors: Mitropoulou, A.N. / Ceska, T. / Heads, J.T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.

History

Deposition	Nov 6, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6tcr.cif.gz	188.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6tcr.ent.gz	147.8 KB	Display	PDB format
PDBx/mmJSON format	6tcr.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/tc/6tcr ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcr	HTTPS FTP

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Related structure data

Related structure data	6tcmSC 6tcnC 6tcoC 6tcpC 6tcqC 6tcsC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4s1d-3 5dq9-1 4dn3-d 6tcm-d 5t6p-2 1um5-d 4r7d-1 5vsh-4 2uyl-1 4gaj-d 6ele-2 6mfj-2 3g6j-4 5i1a-2 6wgk-1 4jzn-1 2hh0-d 3l7f-3 1u6a-d 5mu2-8 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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)

Deposited unit

H: Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

L: Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant

hetero molecules

49.3 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)	43.719, 96.250, 103.300
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant Mass: 24672.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Omalizumab Fab heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody	Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant Mass: 24005.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain mutant Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH7, 20% PEG 4000 and 0.15M ammonium sulphate. Crystals were cryoprotected with 0.1M HEPES pH7.5, 20% PEG 4000, 0.1M ammonium sulphate and 15% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.45→33.37 Å / Num. obs: 77845 / % possible obs: 99.6 % / Redundancy: 6.8 % / B_iso Wilson estimate: 11.2 Å² / R_merge(I) obs: 0.079 / R_pim(I) all: 0.031 / Net I/σ(I): 14.8
Reflection shell	Resolution: 1.45→1.53 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.475 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10961 / R_pim(I) all: 0.25 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TCM

6tcm

Resolution: 1.45→33.37 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.81

	R_factor	Num. reflection	% reflection
R_free	0.1836	3888	5.01 %
R_work	0.166	-	-
obs	0.1669	77571	99.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 85.84 Å² / B_iso mean: 20.6456 Å² / B_iso min: 6.47 Å²

Refinement step

Cycle: final / Resolution: 1.45→33.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3224	0	51	341	3616
B_iso mean	-	-	35.56	31.24	-
Num. residues	-	-	-	-	429

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	3474
X-RAY DIFFRACTION	f_angle_d	1.482	4764
X-RAY DIFFRACTION	f_chiral_restr	0.123	538
X-RAY DIFFRACTION	f_plane_restr	0.01	608
X-RAY DIFFRACTION	f_dihedral_angle_d	15.809	1270

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.45-1.4677	0.2658	139	0.2402	2431	93
1.4677-1.4863	0.2827	130	0.2372	2476	96
1.4863-1.5058	0.2608	142	0.2203	2589	98
1.5058-1.5264	0.2585	130	0.2127	2558	99
1.5264-1.5483	0.2628	154	0.1981	2583	99
1.5483-1.5714	0.2308	148	0.1938	2608	100
1.5714-1.5959	0.2015	132	0.1803	2587	99
1.5959-1.6221	0.2122	142	0.1775	2647	100
1.6221-1.6501	0.2064	157	0.1713	2560	100
1.6501-1.6801	0.2049	158	0.1774	2625	99
1.6801-1.7124	0.223	132	0.1682	2580	100
1.7124-1.7473	0.1745	149	0.1631	2635	100
1.7473-1.7853	0.1577	140	0.1539	2620	100
1.7853-1.8268	0.1847	124	0.1558	2640	100
1.8268-1.8725	0.1903	146	0.1583	2611	100
1.8725-1.9231	0.2084	141	0.1557	2624	100
1.9231-1.9797	0.2071	127	0.1613	2645	100
1.9797-2.0436	0.1731	132	0.1608	2648	100
2.0436-2.1166	0.1759	120	0.1636	2677	100
2.1166-2.2014	0.1743	121	0.157	2676	100
2.2014-2.3015	0.1701	139	0.1667	2659	100
2.3015-2.4229	0.1749	124	0.1673	2664	100
2.4229-2.5746	0.1901	128	0.172	2686	100
2.5746-2.7733	0.1875	160	0.1756	2650	100
2.7733-3.0522	0.2012	133	0.1746	2671	100
3.0522-3.4935	0.1826	129	0.1653	2719	100
3.4935-4.3998	0.1648	143	0.1441	2766	100
4.3998-33.37	0.1409	168	0.1559	2848	100

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	0.2067	0.182	0.1716	0.1361	-0.0703	0.21	0.1164	0.1479	0.0008	0.0015	-0.1997	0.2083	0.0362	-0.2354	0.005	0.1487	0.0283	0.0013	0.1574	-0.0243	0.1322	-17.2601	4.363	-10.4109
2	0.2697	0.1237	-0.1656	0.4488	0.2959	0.385	0.084	0.1638	0.0376	-0.0922	-0.0498	-0.1792	-0.011	-0.0832	0.0223	0.1029	0.0354	0.0222	0.1069	0.0177	0.085	-8.46	8.3415	-13.2482
3	0.0197	0.0174	-0.0186	0.0947	-0.0652	0.0698	0.1063	0.0245	0.0484	-0.1373	-0.0764	-0.119	0.0898	0.0012	0.0027	0.1533	0.0731	0.0231	0.1629	-0.014	0.0871	-9.3027	0.1942	-15.4139
4	0.4165	-0.1591	0.0574	0.0434	-0.0164	0.1338	0.0327	0.0791	0.0438	0.0282	-0.0765	-0.041	0.0436	0.0051	-0.0154	0.0931	0.0172	0.0114	0.0732	0.0066	0.1133	-10.6002	9.846	-4.9847
5	0.3788	0.1304	0.325	0.2231	-0.0107	0.3554	-0.0707	-0.1646	0.1031	-0.0138	-0.0407	0.0445	0.0028	-0.0565	-0.0414	0.1208	0.0066	0.0155	0.1518	-0.0304	0.1009	-15.2409	-16.7828	6.3324
6	0.1242	-0.0068	-0.0369	0.0288	-0.0506	0.1081	-0.3603	-0.2322	0.2951	-0.1167	0.0929	0.0144	-0.1217	-0.2899	-0.0267	-0.2104	0.1684	0.428	0.3656	-0.2332	-0.4076	-20.8754	-16.453	17.2504
7	0.0366	-0.02	0.0025	0.1076	0.1068	0.1074	-0.0453	-0.1524	0.1851	-0.1426	-0.1072	0.1981	-0.0716	-0.2944	-0.0208	0.1107	-0.006	0.015	0.2573	-0.0341	0.146	-23.4826	-16.9702	4.739
8	0.154	0.0367	0.0387	0.1052	-0.0123	0.0428	0.0116	-0.0347	0.024	0.0794	-0.063	-0.1622	0.0503	0.122	0.0003	0.1135	0.016	-0.0074	0.1201	0.0073	0.1274	4.7392	10.6352	10.3069
9	0.2107	-0.0115	0.1917	0.0506	0.0054	0.2019	0.0278	0.0237	0.0784	-0.0161	0.0024	-0.0276	0.0431	-0.0081	0.0227	0.0673	0.0006	0.0027	0.0698	0.0139	0.1051	-3.1587	16.0075	2.2476
10	0.0318	0.1249	-0.002	0.1891	-0.0545	0.2221	0.0332	-0.0194	0.0935	0.0656	0.0324	-0.0199	0.0104	-0.0308	0.045	0.0759	-0.0014	0.0057	0.0879	0.0108	0.112	-4.1652	15.4147	10.7366
11	0.0576	0.009	-0.0158	0.0446	0.0665	0.0542	0.003	0.0609	-0.0154	-0.0174	0.1032	0.0375	0.023	0.0469	0.0186	0.0819	0.0045	0.0091	0.0975	0.028	0.1415	1.1703	13.9225	-5.0731
12	0.0308	-0.0465	-0.003	0.0034	-0.0713	-0.014	0.076	0.0545	0.042	0.0851	-0.0923	0.0231	-0.0827	0.071	-0	0.18	-0.0035	-0.004	0.1522	0.0005	0.1106	-1.5432	-1.9896	22.0257
13	0.0738	-0.0889	0.0372	0.0841	-0.0862	0.0458	0.0709	-0.1411	-0.0941	-0.0058	0.1453	0.2074	-0.0853	-0.1923	0.003	0.175	-0.0661	-0.0154	0.1871	0.0235	0.1441	-14.7247	-28.0062	14.2216
14	0.0124	-0.0245	0.0812	0.0169	0.0483	0.0554	-0.0423	-0.1024	-0.0119	-0.1438	0.0795	0.0263	0.0014	0.0724	-0	0.1577	-0.007	0.0062	0.158	-0.0198	0.0992	-3.9505	-19.4451	18.6717
15	0.0569	0.0423	0.0719	0.0187	0.0418	0.0549	-0.0282	-0.0751	-0.0212	0.0498	-0.0493	-0.1388	-0.0569	0.1204	-0	0.1885	0.0118	0.0083	0.1714	0.0278	0.1252	-0.1765	-26.3321	14.1567
16	-0	0.004	0.0022	0.0153	-0.0068	0.0059	0.0062	0.0888	0.1265	-0.2065	-0.108	0.3421	-0.1499	-0.1331	0.0023	0.2373	0.0069	-0.0477	0.1247	-0.0338	0.1739	-8.0565	-4.4459	18.5405
17	0.1572	-0.1414	0.075	0.1848	-0.0886	0.0828	-0.0601	-0.1786	-0.0744	-0.0078	0.1543	-0.1151	0.1028	0.0203	0.0033	0.1793	-0.0035	-0.0036	0.13	0.0002	0.115	-5.2082	-28.2293	19.5562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 34 )	H	1 - 34
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 35 through 76 )	H	35 - 76
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 77 through 91 )	H	77 - 91
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 92 through 119 )	H	92 - 119
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 183 )	H	120 - 183
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 184 through 202 )	H	184 - 202
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 203 through 221 )	H	203 - 221
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 1 through 25 )	L	1 - 25
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 26 through 52 )	L	26 - 52
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 53 through 94 )	L	53 - 94
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 95 through 105 )	L	95 - 105
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 106 through 117 )	L	106 - 117
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 118 through 132 )	L	118 - 132
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 133 through 154 )	L	133 - 154
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 155 through 167 )	L	155 - 167
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 168 through 178 )	L	168 - 178
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 179 through 216 )	L	179 - 216

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