PDB-6tcq: Crystal structure of the omalizumab Fab Ser81Arg and Gln83Arg lig...

ID or keywords:

Entry

Database: PDB / ID: 6tcq

Title

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

Components

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

Keywords

IMMUNE SYSTEM / Fab / Antibody / immunoglobulin

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6tcq.cif.gz	185.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6tcq.ent.gz	144.6 KB	Display	PDB format
PDBx/mmJSON format	6tcq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6tcq_validation.pdf.gz	437.4 KB	Display	wwPDB validaton report
Full document	6tcq_full_validation.pdf.gz	438.8 KB	Display
Data in XML	6tcq_validation.xml.gz	20 KB	Display
Data in CIF	6tcq_validation.cif.gz	29.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcq ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcq	HTTPS FTP

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Related structure data

Related structure data	6tcmSC 6tcnC 6tcoC 6tcpC 6tcrC 6tcsC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tcn-2 4g6k-d 4kuz-d 4imk-1 5tdo-1 5ewi-d 4x7s-d 1bln-1 5kvl-d 6cdm-1 3if1-2 1aif-2 3l7f-2 2gfb-1 6dwa-2 5mu0-4 1ct8-3 6ks2-1 5mub-2 3hmw-d 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 and Gln83Arg light chain mutant

L: Omalizumab Fab Ser81Arg and Gln83Arg light chain mutant

hetero molecules

48.8 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)	44.033, 96.615, 103.509
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 and Gln83Arg 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 and Gln83Arg light chain mutant Mass: 24021.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Omalizumab Fab Ser81Arg and Gln83Arg light chain mutant Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.26 Å³/Da / Density % sol: 45.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH7 and 20% PEG 4000. Crystals were cryoprotected with 12% PEG 400 and 17% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.05→28.08 Å / Num. obs: 28445 / % possible obs: 99.7 % / Redundancy: 7.5 % / B_iso Wilson estimate: 17.4 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.197 / R_pim(I) all: 0.075 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.889 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2108 / CC_1/2: 0.608 / R_pim(I) all: 0.466 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
PDB_EXTRACT	3.25	data extraction
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TCM

6tcm

Resolution: 2.05→28.077 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.33

	R_factor	Num. reflection	% reflection
R_free	0.2214	1409	4.96 %
R_work	0.1735	-	-
obs	0.1759	28385	99.67 %

Solvent computation

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

Displacement parameters

B_iso max: 79.68 Å² / B_iso mean: 23.8422 Å² / B_iso min: 7.69 Å²

Refinement step

Cycle: final / Resolution: 2.05→28.077 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3248	0	6	304	3558
B_iso mean	-	-	45.81	30.69	-
Num. residues	-	-	-	-	434

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3370
X-RAY DIFFRACTION	f_angle_d	0.954	4608
X-RAY DIFFRACTION	f_chiral_restr	0.056	514
X-RAY DIFFRACTION	f_plane_restr	0.006	592
X-RAY DIFFRACTION	f_dihedral_angle_d	12.394	2000

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 (%)
2.05-2.1232	0.3015	137	0.227	2575	97
2.1232-2.2082	0.2566	135	0.2131	2664	100
2.2082-2.3087	0.2738	143	0.1889	2675	100
2.3087-2.4303	0.269	137	0.187	2656	100
2.4303-2.5825	0.2627	144	0.1861	2678	100
2.5825-2.7817	0.2243	135	0.1815	2691	100
2.7817-3.0614	0.2405	138	0.1774	2678	100
3.0614-3.5036	0.2096	144	0.173	2713	100
3.5036-4.4114	0.1794	148	0.1444	2770	100
4.4114-28.077	0.1847	148	0.1591	2876	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	0.5351	0.0646	-0.3025	0.3069	0.2619	0.3227	0.1651	0.0579	0.1056	-0.0258	-0.0144	-0.1788	-0.2313	0.1688	0.154	0.2458	0.0145	0.0268	0.1622	0.0188	0.1513	14.7141	1.9488	-9.9596
2	0.1166	0.2002	-0.0322	0.233	-0.0993	0.2234	0.2326	0.4131	-0.3788	-0.1513	-0.3463	-0.3995	-0.1931	0.12	-0.0043	0.1916	0.028	0.0187	0.3329	-0.0268	0.2759	20.1985	-10.7765	-9.7671
3	0.3181	0.2314	-0.3916	0.1587	-0.2689	0.3354	0.2975	0.0376	0.0299	-0.302	-0.1147	0.1212	-0.2639	-0.0363	0.0214	0.1655	0.0256	0.0067	0.1235	-0.0029	0.1152	6.4105	-6.3397	-7.5826
4	0.2178	0.1999	0.1269	0.2462	-0.0476	0.3376	0.1072	0.3651	-0.4054	-0.7171	0.0965	0.3656	0.6039	-0.3581	0.0036	0.3602	0.0682	-0.102	0.2309	-0.0334	0.2065	5.5225	-11.4746	-17.2182
5	0.1024	0.1958	0.3235	0.6465	0.0659	0.9535	-0.0148	-0.0835	-0.1839	-0.0861	-0.0195	0.1585	-0.1601	0.0959	0	0.1806	0.0089	0.0058	0.202	0.0168	0.1502	12.1916	-3.5346	-16.2359
6	0.5754	0.0124	-0.0923	0.3177	-0.02	0.5697	0.0987	0.0936	-0.2516	-0.0334	-0.1129	0.2818	0.0054	-0.0168	-0.0104	0.0915	0.0193	-0.0117	0.1075	-0.0162	0.1408	10.3642	-14.2933	-4.4395
7	0.1949	0.2602	-0.0226	0.2533	0.1629	0.0817	-0.017	0.0987	0.0402	-0.1641	0.011	0.0412	-0.1409	0.0107	-0	0.2333	-0.003	-0.0113	0.1477	0.032	0.1933	11.6207	11.3266	-7.3401
8	0.0446	-0.0538	-0.059	0.4169	0.1748	0.0807	-0.2388	-0.3944	0.1022	0.0013	0.0993	-0.0925	-0.6378	-0.0161	0.0325	0.2156	0.0029	-0.0689	0.3171	0.0033	0.1873	17.2071	21.3347	12.2845
9	0.4306	0.2613	-0.5132	0.8082	0.0267	0.6754	-0.1863	-0.1963	-0.0899	-0.0634	0.0017	-0.0543	0.0737	0.2418	-0.1362	0.168	0.0478	0.0227	0.2349	0.0429	0.1559	15.8016	14.2615	10.014
10	0.2279	0.3221	0.1725	0.8297	0.3268	1.0718	-0.2541	-0.4595	-0.0897	-0.3856	-0.0303	-0.3197	-0.3967	0.265	-0.0056	0.1041	0.0401	-0.0004	0.4006	0.0557	0.2283	24.8204	17.5071	8.3936
11	0.8833	-0.296	-0.397	0.2738	0.1899	0.2899	-0.0109	-0.0747	-0.1211	0.118	0.0054	0.2978	-0.1631	-0.2066	0.0504	0.158	0.0087	0.0504	0.1588	0.0097	0.195	-4.6366	-10.7952	10.6719
12	1.1932	-0.1131	-0.6006	0.1854	0.0103	0.4513	0.021	0.1564	-0.1184	0.0151	0.029	0.006	-0.0031	0.0951	0.0611	0.0813	-0.0074	-0.0002	0.0988	-0.0084	0.1226	3.1023	-16.0721	2.2354
13	0.241	-0.1036	-0.0785	-0.006	0.1273	0.7034	0.0935	-0.0784	-0.1486	0.1956	0.0438	-0.0303	0.1837	-0.0221	0.0588	0.0889	-0.0029	-0.0142	0.109	0.0116	0.1588	3.9665	-19.663	9.4996
14	0.2809	0.0613	0.2065	0.7675	-0.2303	0.7563	0.0543	0.027	-0.1332	0.0252	0.1124	0.0306	-0.0583	0.0444	0.0573	0.0849	0.011	0.0296	0.1227	0.0039	0.1613	2.3675	-11.1512	5.5449
15	0.0659	-0.0792	0.1868	0.0684	0.0154	0.0591	0.0705	-0.0805	-0.2164	0.1479	0.0376	-0.2285	0.2555	0.2072	-0.0001	0.2085	-0.014	0.0254	0.1919	0.0123	0.1217	1.6608	1.7736	22.066
16	0.2755	0.1448	-0.3614	0.6973	-0.0367	1.3623	-0.0058	-0.2989	0.1167	0.0665	0.0577	-0.0405	-0.3448	0.1285	0.0739	0.2506	-0.0306	-0.0309	0.186	-0.0099	0.1636	8.3107	22.6283	16.8431
17	0.9311	1.0187	-0.5368	0.753	-0.591	0.4382	-0.0224	-0.0182	0.025	0.0095	-0.0993	-0.1968	0.0055	-0.0842	-0.0017	0.2279	0.0403	0.0012	0.1777	-0.0178	0.1399	4.1617	15.5014	16.2585
18	1.045	-0.6445	-0.1091	0.591	-0.1968	0.5288	-0.0613	-0.2557	0.2595	0.2208	0.0848	0.0713	-0.4715	0.0879	0.0142	0.3432	-0.0178	-0.0423	0.1532	-0.0506	0.166	5.5345	28.51	19.5457

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 17 )	H	1 - 17
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 33 )	H	18 - 33
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 34 through 52 )	H	34 - 52
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 53 through 67 )	H	53 - 67
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 68 through 91 )	H	68 - 91
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 92 through 111 )	H	92 - 111
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 112 through 127 )	H	112 - 127
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 128 through 153 )	H	128 - 153
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 154 through 197 )	H	154 - 197
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 198 through 222 )	H	198 - 222
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 1 through 25 )	L	1 - 25
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 26 through 52 )	L	26 - 52
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 53 through 79 )	L	53 - 79
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 80 through 105 )	L	80 - 105
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 106 through 117 )	L	106 - 117
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 118 through 154 )	L	118 - 154
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 155 through 178 )	L	155 - 178
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 179 through 217 )	L	179 - 217

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