PDB-3qpq: Crystal structure of ANTI-TLR3 antibody C1068 FAB

ID or keywords:

Entry

Database: PDB / ID: 3qpq

Title

Crystal structure of ANTI-TLR3 antibody C1068 FAB

Components

C1068 heavy chain
C1068 light chain

Keywords

IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / TLR-3

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Luo, J. / Obmolova, G. / Teplyakov, A. / Gilliland, G.L.

Citation

Journal: To be Published
Title: Crystal structure of Fab C1068
Authors: Luo, J. / Teplyakov, A. / Obmolova, G. / Gilliland, G.L.

History

Deposition	Feb 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qpq.cif.gz	692.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3qpq.ent.gz	577.2 KB	Display	PDB format
PDBx/mmJSON format	3qpq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3qpq_validation.pdf.gz	512.7 KB	Display	wwPDB validaton report
Full document	3qpq_full_validation.pdf.gz	542.9 KB	Display
Data in XML	3qpq_validation.xml.gz	85.3 KB	Display
Data in CIF	3qpq_validation.cif.gz	122.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qp/3qpq ftp://data.pdbj.org/pub/pdb/validation_reports/qp/3qpq	HTTPS FTP

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Related structure data

Similar structure data	5jop-1 1xf4-2 4x80-d 5hdb-4 6i1o-d 5szf-d 5gir-1 4kk9-2 3ojd-d 2a77-d 3ejz-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

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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: C1068 light chain

H: C1068 heavy chain

E: C1068 light chain

F: C1068 heavy chain

C: C1068 light chain

D: C1068 heavy chain

I: C1068 light chain

J: C1068 heavy chain

hetero molecules

193 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: C1068 light chain

H: C1068 heavy chain

hetero molecules

defined by author&software
48.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: C1068 light chain

F: C1068 heavy chain

hetero molecules

defined by author&software
48.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: C1068 light chain

D: C1068 heavy chain

hetero molecules

defined by author&software
48.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

I: C1068 light chain

J: C1068 heavy chain

hetero molecules

defined by author&software
48.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.480, 136.940, 83.250
Angle α, β, γ (deg.)	90.00, 114.95, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	C1068 light chain Mass: 23606.135 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens, Mus musculus / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#2: Antibody	C1068 heavy chain Mass: 24285.299 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens, Mus musculus / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1701 / Source method: isolated from a natural source / Formula: H₂O
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: 2.23 Å³/Da / Density % sol: 44.72 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 22% PEG 8000, 0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 9, 2006 / Details: VARIMAX HF
Radiation	Monochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 119205 / Num. obs: 119205 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / B_iso Wilson estimate: 28.3 Å² / R_merge(I) obs: 0.12

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_601)	refinement
CNX		refinement
StructureStudio		data collection
d*TREK		data reduction
d*TREK		data scaling
CNX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→44.553 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 29.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2556	5914	5.04 %
R_work	0.2014	-	-
obs	0.2041	117268	89.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.2 Å² / k_sol: 0.389 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.5578 Å²	0 Å²	-5.6867 Å²
2-	-	-5.7721 Å²	-0 Å²
3-	-	-	1.2143 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→44.553 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13312	0	107	1701	15120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13899
X-RAY DIFFRACTION	f_angle_d	1.111	18912
X-RAY DIFFRACTION	f_dihedral_angle_d	13.948	4991
X-RAY DIFFRACTION	f_chiral_restr	0.074	2128
X-RAY DIFFRACTION	f_plane_restr	0.005	2404

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 (%)
1.9-1.9215	0.449	90	0.4253	1577	X-RAY DIFFRACTION	38
1.9215-1.9442	0.4949	88	0.3741	1873	X-RAY DIFFRACTION	45
1.9442-1.9679	0.3821	97	0.3278	2159	X-RAY DIFFRACTION	52
1.9679-1.9928	0.3949	146	0.3039	2433	X-RAY DIFFRACTION	59
1.9928-2.019	0.3443	164	0.2725	2748	X-RAY DIFFRACTION	66
2.019-2.0467	0.3525	169	0.2717	3050	X-RAY DIFFRACTION	74
2.0467-2.0759	0.328	184	0.2455	3401	X-RAY DIFFRACTION	81
2.0759-2.1069	0.3452	188	0.2408	3626	X-RAY DIFFRACTION	88
2.1069-2.1398	0.2898	198	0.2419	3929	X-RAY DIFFRACTION	95
2.1398-2.1749	0.2884	217	0.235	4105	X-RAY DIFFRACTION	98
2.1749-2.2124	0.3159	225	0.2149	4111	X-RAY DIFFRACTION	100
2.2124-2.2526	0.3125	238	0.222	4158	X-RAY DIFFRACTION	100
2.2526-2.2959	0.2993	242	0.2259	4115	X-RAY DIFFRACTION	100
2.2959-2.3428	0.3198	194	0.2237	4163	X-RAY DIFFRACTION	100
2.3428-2.3937	0.3004	224	0.2296	4155	X-RAY DIFFRACTION	100
2.3937-2.4494	0.3056	195	0.2195	4179	X-RAY DIFFRACTION	100
2.4494-2.5107	0.3067	207	0.2154	4152	X-RAY DIFFRACTION	100
2.5107-2.5785	0.2721	248	0.2142	4154	X-RAY DIFFRACTION	100
2.5785-2.6544	0.268	219	0.2159	4121	X-RAY DIFFRACTION	100
2.6544-2.7401	0.2865	215	0.2066	4162	X-RAY DIFFRACTION	100
2.7401-2.838	0.2653	207	0.2117	4164	X-RAY DIFFRACTION	100
2.838-2.9516	0.2753	221	0.2138	4186	X-RAY DIFFRACTION	100
2.9516-3.0859	0.2475	199	0.1993	4174	X-RAY DIFFRACTION	100
3.0859-3.2485	0.2653	242	0.1923	4120	X-RAY DIFFRACTION	100
3.2485-3.452	0.2334	220	0.1878	4169	X-RAY DIFFRACTION	100
3.452-3.7184	0.2278	217	0.1715	4150	X-RAY DIFFRACTION	99
3.7184-4.0924	0.1793	216	0.1547	4086	X-RAY DIFFRACTION	98
4.0924-4.684	0.1626	222	0.1359	3949	X-RAY DIFFRACTION	95
4.684-5.8992	0.2046	210	0.1663	4020	X-RAY DIFFRACTION	96
5.8992-44.553	0.29	212	0.2649	3965	X-RAY DIFFRACTION	93

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	0.0556	-0.0583	0.1042	0.4871	-0.0877	0.458	0.0283	0.0025	0.0451	0.0546	-0.0222	-0.0354	0.0293	0.0579	-0.0199	0.0952	-0.0115	0.0114	0.1324	0.0113	0.1318	111.1456	33.9218	46.6848
2	0.1966	-0.1101	0.0812	0.2761	0.0367	0.1169	0.0221	-0.0091	-0.0529	-0.2329	-0.0325	-0.0236	-0.1358	0.0094	-0.0099	0.0986	-0.004	0.026	0.0525	-0.0301	0.0754	101.8616	-1.3339	44.1046
3	0.482	0.2123	0.2072	0.9216	0.4364	0.5791	0.0628	0.0667	-0.0217	-0.0328	-0.0765	-0.0052	0.1029	-0.0642	0.0052	0.1161	0.0065	0.01	0.1358	-0.0114	0.1004	96.4659	36.6701	30.0408
4	0.1292	-0.1055	0.0491	0.1521	-0.0047	0.4033	-0.0039	-0.0131	-0.2308	0.005	0.0847	0.0922	-0.0176	-0.2158	-0.053	0.1244	0.0104	0.0235	0.2178	0.0062	0.1728	87.0608	5.1558	44.4116
5	0.4868	0.3175	0.275	0.8292	0.1049	0.3637	-0.0327	0.0188	0.1125	-0.004	0.0357	0.1052	-0.0135	0.0235	0.0045	0.1883	-0.0295	-0.024	0.1327	-0.0118	0.1534	50.7521	46.48	85.0842
6	0.4673	-0.1412	0.3014	0.838	-0.3585	0.3319	0.0288	0.0191	-0.0153	-0.1482	0.0065	0.0385	0.0662	0.0205	-0.0333	0.1734	0.0151	-0.0048	0.1401	0.0082	0.1231	54.4226	81.0336	74.4423
7	0.1774	-0.0271	0.0521	0.5553	0.049	0.2649	-0.1454	0.1482	0.0953	-0.2238	0.3492	0.4889	0.0282	0.0636	0.0876	0.2384	-0.095	-0.1463	0.0596	0.1024	0.2004	41.5484	43.6707	64.7803
8	0.3303	-0.2141	0.2421	0.402	-0.4794	0.5087	0.0943	0.1171	-0.118	-0.2231	-0.0248	0.0283	0.2148	0.122	-0.0472	0.2482	0.041	-0.0142	0.1968	-0.0311	0.1507	58.3117	72.2524	61.7821
9	0.0212	-0.0257	0.1492	0.8066	-0.2359	0.7838	0.01	-0.0043	-0.0544	0.0001	0.0093	-0.1326	0.1138	0.0683	-0.0252	0.1068	-0.004	-0.0005	0.1276	0.0058	0.1689	69.6559	34.6849	46.8527
10	0.0218	-0.0684	-0.0078	1.0948	-0.0325	0.5334	0.0132	-0.0031	0.0176	-0.0933	0.0342	0.0191	-0.0918	0.0395	-0.0489	0.1462	0.0119	-0.003	0.1441	-0.0188	0.1599	60.3637	-0.6095	44.1141
11	0.463	0.4749	0.4114	0.5781	0.2978	0.5955	-0.0509	0.0845	-0.0402	-0.0511	0.0761	-0.0148	-0.0045	0.0443	-0.0226	0.1324	-0.0271	0.0167	0.1843	0.0017	0.1472	55.9356	37.4455	29.3883
12	0.0565	-0.0266	-0.0798	0.5298	0.4232	0.3255	0.0561	0.0774	-0.1022	-0.0577	0.0762	0.0263	-0.0695	-0.2523	-0.0963	0.1303	0.0367	0.0228	0.2548	0.059	0.1511	45.8662	6.094	43.0369
13	0.7244	0.5907	0.2185	1.0248	0.0681	0.1162	0.1116	-0.0678	0.0137	0.3685	-0.1447	-0.0088	0.01	0.004	0.0336	0.189	-0.047	0.0137	0.1299	-0.0084	0.1343	10.8509	47.0351	84.1641
14	0.1979	-0.0588	-0.027	0.4954	0.0345	0.4267	0.1114	-0.0092	-0.0691	-0.105	-0.0473	0.1649	0.0069	0.0303	-0.0605	0.1812	0.0424	-0.0054	0.1406	0.0031	0.1584	15.1052	82.4679	73.8686
15	0.4663	-0.3385	0.2691	0.5627	0.0758	0.294	-0.0212	0.0045	-0.2982	-0.2618	0.0025	0.6758	-0.0089	-0.0712	-0.0322	0.0795	0.0213	-0.0447	0.122	0.0057	0.2505	3.0295	44.596	63.5499
16	0.8284	0.4359	0.2132	0.894	0.1262	0.0933	-0.0936	-0.0045	0.0915	-0.2378	0.0636	0.0823	-0.1506	0.0689	0.0128	0.1989	0.0158	-0.0022	0.1871	-0.0235	0.1444	21.4849	75.5353	60.8859

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain L and resseq 1:110
2	X-RAY DIFFRACTION	2	chain L and resseq 111:215
3	X-RAY DIFFRACTION	3	chain H and resseq 1:120
4	X-RAY DIFFRACTION	4	chain H and resseq 121:217
5	X-RAY DIFFRACTION	5	chain E and resseq 1:110
6	X-RAY DIFFRACTION	6	chain E and resseq 111:215
7	X-RAY DIFFRACTION	7	chain F and resseq 1:120
8	X-RAY DIFFRACTION	8	chain F and resseq 121:217
9	X-RAY DIFFRACTION	9	chain C and resseq 1:110
10	X-RAY DIFFRACTION	10	chain C and resseq 111:215
11	X-RAY DIFFRACTION	11	chain D and resseq 1:120
12	X-RAY DIFFRACTION	12	chain D and resseq 121:217
13	X-RAY DIFFRACTION	13	chain I and resseq 1:110
14	X-RAY DIFFRACTION	14	chain I and resseq 111:215
15	X-RAY DIFFRACTION	15	chain J and resseq 1:120
16	X-RAY DIFFRACTION	16	chain J and resseq 121:217

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