PDB-3qq9: Crystal structure of FAB fragment of anti-human RSV (RESPIRATORY ...

ID or keywords:

Entry

Database: PDB / ID: 3qq9

Title

Crystal structure of FAB fragment of anti-human RSV (RESPIRATORY SYNCYTIAL VIRUS) F Protein MAB 101F

Components

101F HEAVY CHAIN
101F LIGHT CHAIN

Keywords

IMMUNE SYSTEM / RSV F protein

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 Å

Authors

Luo, J. / Tsui, P. / Spurlino, J. / Lewansowski, F. / Heavner, G.A. / Del Vecchio, F.

Citation

Journal: To be Published
Title: Crystal Structure of Fab 101F
Authors: Luo, J. / Tsui, P. / Spurlino, J. / Lewansowski, F. / Heavner, G.A. / Del Vecchio, F.

History

Deposition	Feb 15, 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	Oct 30, 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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PDBx/mmCIF format	3qq9.cif.gz	510.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3qq9_validation.pdf.gz	469.4 KB	Display	wwPDB validaton report
Full document	3qq9_full_validation.pdf.gz	483.9 KB	Display
Data in XML	3qq9_validation.xml.gz	48.6 KB	Display
Data in CIF	3qq9_validation.cif.gz	73.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qq/3qq9 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qq9	HTTPS FTP

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Related structure data

Similar structure data	5fgb-1 1mjj-2 3l7f-3 5mv4-8 1rz8-2 1aj7-d 5trp-d 2eh8-d 6dca-2 6med-1 5mp1-3 6wkm-d 5mp5-4 6b5l-d 6wg0-d 5jrp-d 3uo1-d 5mvj-4 1a3l-d 4gaj-d 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: 101F LIGHT CHAIN

H: 101F HEAVY CHAIN

C: 101F LIGHT CHAIN

D: 101F HEAVY CHAIN

hetero molecules

96.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: 101F LIGHT CHAIN

H: 101F HEAVY CHAIN

hetero molecules

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

2

C: 101F LIGHT CHAIN

D: 101F 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)	113.306, 84.558, 101.658
Angle α, β, γ (deg.)	90.00, 104.87, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	L-547- HOH

#1: Antibody	101F LIGHT CHAIN Mass: 23895.523 Da / Num. of mol.: 2 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	101F HEAVY CHAIN Mass: 24326.340 Da / Num. of mol.: 2 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1236 / 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: 2.44 Å³/Da / Density % sol: 49.59 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1M Ammonium Sulphate, 0.2M Lithium Sulfate, Sodium Actate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2005
Radiation	Monochromator: Accel, double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.64→50 Å / Num. all: 96655 / Num. obs: 96655 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / R_merge(I) obs: 0.034

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.6.4_486)	refinement
CNX		refinement
ADSC	Quantum	data collection
HKL-2000		data reduction
HKL-2000		data scaling
CNX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.64→42.367 Å / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2171	4846	5.01 %	Random
R_work	0.173	-	-	-
obs	0.1752	96642	85.1 %	-
all	-	96642	-	-

Solvent computation

Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 74.078 Å² / k_sol: 0.514 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.8283 Å²	-0 Å²	-5.4159 Å²
2-	-	-0.5937 Å²	0 Å²
3-	-	-	4.422 Å²

Refinement step

Cycle: LAST / Resolution: 1.64→42.367 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6583	0	25	1236	7844

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	6861
X-RAY DIFFRACTION	f_angle_d	1.527	9366
X-RAY DIFFRACTION	f_dihedral_angle_d	13.436	2466
X-RAY DIFFRACTION	f_chiral_restr	0.112	1058
X-RAY DIFFRACTION	f_plane_restr	0.008	1195

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 (%)
1.64-1.6578	0.2562	78	0.2149	1618	X-RAY DIFFRACTION	45
1.6578-1.6773	0.2608	84	0.2101	1793	X-RAY DIFFRACTION	50
1.6773-1.6977	0.2477	98	0.2107	1980	X-RAY DIFFRACTION	55
1.6977-1.7192	0.2159	125	0.1997	2206	X-RAY DIFFRACTION	61
1.7192-1.7419	0.2731	137	0.1973	2386	X-RAY DIFFRACTION	67
1.7419-1.7657	0.2809	128	0.1866	2620	X-RAY DIFFRACTION	73
1.7657-1.7909	0.214	142	0.1992	2799	X-RAY DIFFRACTION	79
1.7909-1.8177	0.2231	154	0.1917	3049	X-RAY DIFFRACTION	84
1.8177-1.8461	0.2583	149	0.1876	3203	X-RAY DIFFRACTION	89
1.8461-1.8763	0.2122	183	0.1834	3349	X-RAY DIFFRACTION	94
1.8763-1.9087	0.2244	191	0.1829	3482	X-RAY DIFFRACTION	97
1.9087-1.9434	0.2051	203	0.1845	3492	X-RAY DIFFRACTION	99
1.9434-1.9808	0.2124	191	0.1727	3579	X-RAY DIFFRACTION	100
1.9808-2.0212	0.2086	211	0.1659	3594	X-RAY DIFFRACTION	100
2.0212-2.0652	0.1941	167	0.1687	3593	X-RAY DIFFRACTION	100
2.0652-2.1132	0.2029	193	0.1688	3587	X-RAY DIFFRACTION	100
2.1132-2.1661	0.1992	205	0.1652	3580	X-RAY DIFFRACTION	100
2.1661-2.2246	0.2408	183	0.1641	3584	X-RAY DIFFRACTION	100
2.2246-2.2901	0.2026	201	0.1659	3544	X-RAY DIFFRACTION	99
2.2901-2.364	0.2277	241	0.1587	3570	X-RAY DIFFRACTION	100
2.364-2.4485	0.1901	180	0.1644	3570	X-RAY DIFFRACTION	100
2.4485-2.5465	0.2139	181	0.1611	3590	X-RAY DIFFRACTION	100
2.5465-2.6624	0.2237	176	0.1657	3602	X-RAY DIFFRACTION	100
2.6624-2.8027	0.1917	185	0.1576	3581	X-RAY DIFFRACTION	99
2.8027-2.9783	0.2127	194	0.1528	3573	X-RAY DIFFRACTION	99
2.9783-3.2081	0.1965	183	0.1547	3518	X-RAY DIFFRACTION	97
3.2081-3.5308	0.2	157	0.1599	3257	X-RAY DIFFRACTION	90
3.5308-4.0414	0.22	128	0.169	2723	X-RAY DIFFRACTION	75
4.0414-5.0904	0.1903	98	0.1918	1977	X-RAY DIFFRACTION	54
5.0904-42.3814	0.3936	100	0.3001	1797	X-RAY DIFFRACTION	49

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	0.3234	0.3551	0.0685	1.503	0.3471	0.9919	-0.0735	-0.007	0.0083	0.0247	0.1403	0.18	0.009	0.0348	-0.0771	0.08	0.0257	0.0356	0.1032	0.0422	0.1894	3.6689	0.5907	56.21
2	1.2949	-0.0542	0.7837	1.3352	0.6354	1.0948	0.1429	0.2987	-0.2519	-0.4752	0.0905	0.1225	0.1533	0.1634	-0.2041	0.2896	-0.0271	-0.072	0.2355	-0.0177	0.1917	-1.7297	11.3737	20.1179
3	0.8979	0.1225	-0.2347	0.5541	-0.2209	0.8173	-0.0591	-0.1115	0.0708	0.0282	0.0808	-0.0207	0.0153	0.0574	-0.0327	0.1334	0.0114	0.0231	0.1478	0.0008	0.195	12.3891	21.07	58.0172
4	0.7581	-0.0166	0.5102	0.6281	0.2134	0.7603	0.0143	0.028	-0.1839	-0.024	0.0323	0.0286	0.0398	-0.1327	-0.0428	0.1623	-0.0419	0.0124	0.209	0.0264	0.1845	-3.5298	24.0245	30.1111
5	0.785	0.1865	0.9967	0.9644	-0.1239	1.8993	-0.1808	0.1787	0.2024	0.1967	-0.205	-0.0829	-0.2063	0.5095	0.3179	0.2744	-0.0318	-0.0744	0.2939	0.101	0.2683	18.0826	13.175	91.011
6	1.0676	0.4901	1.0952	1.324	0.8262	1.6169	-0.1602	-0.2847	0.2163	-0.1052	-0.1777	0.0195	-0.2621	-0.2952	0.2896	0.2534	0.0797	-0.0494	0.2814	-0.0993	0.2374	18.1767	5.1839	127.2745
7	0.4903	0.1162	0.1526	1.2214	-0.8608	1.034	0.0852	0.0085	-0.0479	-0.1322	-0.0781	-0.0012	0.1983	0.0158	-0.0246	0.3043	0.0453	-0.0229	0.204	0.0016	0.1663	1.2033	-1.802	90.547
8	0.7743	0.4233	0.4375	0.439	0.3103	2.1858	-0.2134	-0.791	0.4467	-0.2126	-0.2635	0.4625	-0.1991	-0.9949	0.462	0.1978	0.2165	-0.1199	0.5638	-0.3037	0.3204	2.4632	7.7252	122.7977

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain L and resseq 1:112 and not element H
2	X-RAY DIFFRACTION	2	chain L and resseq 113:217 and not element H
3	X-RAY DIFFRACTION	3	chain H and resseq 1:120 and not element H
4	X-RAY DIFFRACTION	4	chain H and resseq 121:220 and not element H
5	X-RAY DIFFRACTION	5	chain C and resseq 1:112 and not element H
6	X-RAY DIFFRACTION	6	chain C and resseq 113:217 and not element H
7	X-RAY DIFFRACTION	7	chain D and resseq 1:120 and not element H
8	X-RAY DIFFRACTION	8	chain D and resseq 121:220 and not element H

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