PDB-5jor: Crystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A

ID or keywords:

Entry

Database: PDB / ID: 5jor

Title

Crystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A

Components

Fab 14.22 light chain
Fab14.22 heavy chain

Keywords

IMMUNE SYSTEM / S. pneumoniae serotype 14 / anti-glycan B cells / synthetic conjugate vaccine / nanomolar affinity anti-glycan antibody / immune system-bacterial glycan complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.206 Å

Authors

Sarkar, A. / Irimia, A. / Teyton, L. / Wilson, I.A.

Citation

Journal: J. Clin. Invest. / Year: 2017
Title: T cells control the generation of nanomolar-affinity anti-glycan antibodies.
Authors: Polonskaya, Z. / Deng, S. / Sarkar, A. / Kain, L. / Comellas-Aragones, M. / McKay, C.S. / Kaczanowska, K. / Holt, M. / McBride, R. / Palomo, V. / Self, K.M. / Taylor, S. / Irimia, A. / ...

History

Deposition	May 2, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2017	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5jor.cif.gz	699.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jo/5jor ftp://data.pdbj.org/pub/pdb/validation_reports/jo/5jor	HTTPS FTP

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Related structure data

Related structure data	5jopC 1qgcS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5tdo-2 6wrp-d 4lkc-d 4xbg-1 3cfb-2 3i75-d 3hr5-1 6azm-2 4yhi-2 3g6j-4 5nb5-1 2gcy-d 5mv3-2 7jwp-1 4xcc-d 5vzr-1 4xxd-1 1nd0-4 1ad0-1 3hns-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) 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

Related structure data

5jopC

1qgcS

C: citing same article (ref.)

S: Starting model for refinement

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

B: Fab14.22 heavy chain

A: Fab 14.22 light chain

F: Fab14.22 heavy chain

H: Fab14.22 heavy chain

L: Fab 14.22 light chain

C: Fab 14.22 light chain

D: Fab14.22 heavy chain

E: Fab 14.22 light chain

hetero molecules

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

1

B: Fab14.22 heavy chain

C: Fab 14.22 light chain

hetero molecules

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

2

A: Fab 14.22 light chain

D: Fab14.22 heavy chain

hetero molecules

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

3

F: Fab14.22 heavy chain

E: Fab 14.22 light chain

hetero molecules

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

4

H: Fab14.22 heavy chain

L: Fab 14.22 light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	120.613, 75.992, 122.946
Angle α, β, γ (deg.)	90.00, 100.58, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Antibody , 2 types, 8 molecules BFHDALCE

#1: Antibody	Fab14.22 heavy chain Mass: 26778.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody	Fab 14.22 light chain Mass: 24436.193 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 946 molecules

#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.34 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1:1 (v/v) protein/reservoir drop equilibrated against 3.6M ammonium sulfate, with 10% PEG400 and 10%MPD, in 1M of HEPES (pH 7.5) reservoir solution

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Data collection

Diffraction	Mean temperature: 293 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03321 Å / Relative weight: 1
Reflection	Resolution: 2.206→49.74 Å / Num. obs: 109255 / % possible obs: 99.4 % / Redundancy: 3.6 % / B_iso Wilson estimate: 37.5 Å² / CC_1/2: 0.902 / R_sym value: 0.013 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.2061→2.2312 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 95.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: 000)	refinement
HKL-2000	v706e	data reduction
HKL-2000	v706e	data scaling
PHASER	2.5.6	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1QGC

1qgc

Resolution: 2.206→49.733 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2369	5450	5 %
R_work	0.2052	-	-
obs	0.2068	109097	98.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.206→49.733 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13202	0	440	879	14521

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13987
X-RAY DIFFRACTION	f_angle_d	0.52	18959
X-RAY DIFFRACTION	f_dihedral_angle_d	10.903	8237
X-RAY DIFFRACTION	f_chiral_restr	0.042	2077
X-RAY DIFFRACTION	f_plane_restr	0.003	2353

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 (%)
2.2061-2.2312	0.3209	158	0.2921	2847	X-RAY DIFFRACTION	81
2.2312-2.2574	0.3323	172	0.2714	3347	X-RAY DIFFRACTION	97
2.2574-2.285	0.3281	171	0.2715	3396	X-RAY DIFFRACTION	98
2.285-2.3139	0.3334	183	0.2678	3419	X-RAY DIFFRACTION	99
2.3139-2.3443	0.2972	181	0.275	3466	X-RAY DIFFRACTION	99
2.3443-2.3764	0.3	182	0.2629	3474	X-RAY DIFFRACTION	100
2.3764-2.4104	0.3322	183	0.2641	3455	X-RAY DIFFRACTION	100
2.4104-2.4464	0.2956	179	0.2521	3479	X-RAY DIFFRACTION	100
2.4464-2.4846	0.3055	183	0.2558	3420	X-RAY DIFFRACTION	100
2.4846-2.5253	0.2894	181	0.2411	3502	X-RAY DIFFRACTION	100
2.5253-2.5689	0.3104	192	0.2419	3457	X-RAY DIFFRACTION	100
2.5689-2.6156	0.292	184	0.2406	3495	X-RAY DIFFRACTION	100
2.6156-2.6659	0.2754	180	0.2321	3441	X-RAY DIFFRACTION	100
2.6659-2.7203	0.2493	184	0.2304	3493	X-RAY DIFFRACTION	100
2.7203-2.7794	0.3229	183	0.2234	3462	X-RAY DIFFRACTION	100
2.7794-2.8441	0.266	192	0.2163	3468	X-RAY DIFFRACTION	100
2.8441-2.9152	0.2529	178	0.2085	3481	X-RAY DIFFRACTION	100
2.9152-2.994	0.248	173	0.2109	3478	X-RAY DIFFRACTION	100
2.994-3.0821	0.2261	187	0.2072	3455	X-RAY DIFFRACTION	99
3.0821-3.1816	0.2445	179	0.2109	3484	X-RAY DIFFRACTION	99
3.1816-3.2953	0.2661	190	0.211	3475	X-RAY DIFFRACTION	99
3.2953-3.4272	0.2568	181	0.1988	3457	X-RAY DIFFRACTION	100
3.4272-3.5831	0.2259	184	0.1862	3476	X-RAY DIFFRACTION	100
3.5831-3.7719	0.2144	181	0.1817	3521	X-RAY DIFFRACTION	100
3.7719-4.0082	0.1784	180	0.1815	3508	X-RAY DIFFRACTION	100
4.0082-4.3175	0.1906	185	0.1646	3503	X-RAY DIFFRACTION	100
4.3175-4.7517	0.1843	190	0.1549	3519	X-RAY DIFFRACTION	100
4.7517-5.4385	0.1718	187	0.1683	3525	X-RAY DIFFRACTION	100
5.4385-6.8491	0.2596	182	0.2166	3562	X-RAY DIFFRACTION	100
6.8491-49.7453	0.2191	185	0.2227	3582	X-RAY DIFFRACTION	98

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	5.597	-0.4649	0.5006	0.5741	-0.2452	2.0857	-0.0139	0.1188	-0.5115	-0.0529	0.0411	0.0776	0.1979	-0.2328	-0.0488	0.4488	-0.0333	0.0348	0.209	0.003	0.2125	-15.4451	-1.3354	-24.4798
2	3.2356	0.9418	-0.2727	0.4951	-0.1084	0.6319	-0.0733	-0.0766	-0.0303	-0.0465	0.0422	-0.0014	0.0111	-0.091	0.0308	0.3505	0.0247	0.0093	0.2404	0.0194	0.2152	-14.1659	1.4472	-6.7642
3	2.4446	0.0375	1.7843	0.4782	0.0182	1.5612	-0.1039	0.2114	0.1397	-0.016	0.0691	0.1055	-0.0753	-0.0141	0.0728	0.3505	-0.0511	0.0321	0.3369	0.0347	0.2373	-23.9875	32.7574	-30.4957
4	1.3192	0.1865	0.9648	0.7756	-0.3494	2.3416	-0.0642	0.0943	0.022	-0.0641	0.0232	-0.0199	0.0953	-0.0094	0.0375	0.2267	0.0005	0.0601	0.2509	0.0078	0.2269	-35.6178	20.0068	-25.9244
5	1.2323	-0.208	1.0026	0.6144	0.0944	2.2278	-0.0792	-0.034	0.0425	0.0177	0.0229	-0.0043	0.1005	0.1212	0.0394	0.245	0.0068	0.0571	0.2714	-0.0231	0.2401	-73.1347	20.6806	-33.9948
6	2.8417	-0.4603	1.7449	0.5837	-0.201	1.8018	-0.1471	-0.244	0.1672	0.0401	0.0903	-0.128	-0.0732	0.0024	0.07	0.3449	0.0467	0.0428	0.3013	-0.046	0.2564	-84.4175	33.2585	-28.5963
7	3.4967	1.1792	-0.6902	0.701	-0.1627	0.8837	-0.0935	0.0095	-0.0953	-0.0668	0.0774	-0.0311	0.0649	-0.1021	0.018	0.3585	0.0216	0.0139	0.1858	0.0304	0.1907	-2.086	40.9033	-65.5859
8	5.1018	-0.0369	0.4357	0.4116	0.03	1.6906	-0.0197	0.2078	-0.5448	-0.0379	0.0691	0.0769	0.3118	-0.2326	-0.0763	0.4593	-0.0662	0.0233	0.2301	0.0054	0.2568	-3.5585	37.0414	-83.3021

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D'
2	X-RAY DIFFRACTION	2	chain 'A'
3	X-RAY DIFFRACTION	3	chain 'H'
4	X-RAY DIFFRACTION	4	chain 'L'
5	X-RAY DIFFRACTION	5	chain 'E'
6	X-RAY DIFFRACTION	6	chain 'F'
7	X-RAY DIFFRACTION	7	chain 'C'
8	X-RAY DIFFRACTION	8	chain 'B'

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