PDB-5t0y: 2A10 Antibody FAB fragment

ID or keywords:

Entry

Database: PDB / ID: 5t0y

Title

2A10 Antibody FAB fragment

Components

2A10 FAB fragment heavy chain
2A10 FAB fragment light chain

Keywords

IMMUNE SYSTEM / Malaria Antibody

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.011 Å

Authors

Jackson, C.J. / Fisher, C.

Citation

Journal: To Be Published
Title: Restricted antibody diversity and low affinity limit antibody responses to the Plasmodium circumsporozoite protein
Authors: Jackson, C.J. / Cockburn, I.

History

Deposition	Aug 17, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 21, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t0y.cif.gz	501.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5t0y.ent.gz	418.1 KB	Display	PDB format
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Validation report

Summary document	5t0y_validation.pdf.gz	468.4 KB	Display	wwPDB validaton report
Full document	5t0y_full_validation.pdf.gz	473.2 KB	Display
Data in XML	5t0y_validation.xml.gz	42.5 KB	Display
Data in CIF	5t0y_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t0/5t0y ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t0y	HTTPS FTP

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Related structure data

Similar structure data	5vh3-1 6xli-1 1kem-d 6bb4-2 4kka-2 1ghf-d 4kjw-2 3nz8-2 6mee-2 6p9i-1 4nki-d 3qpq-4 5xhg-1 3kym-4 1hil-2 1a4k-1 1rzg-1 6idh-d 3i9g-d 6ugu-1 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: 2A10 FAB fragment light chain

H: 2A10 FAB fragment heavy chain

B: 2A10 FAB fragment light chain

A: 2A10 FAB fragment heavy chain

G: 2A10 FAB fragment light chain

I: 2A10 FAB fragment heavy chain

hetero molecules

142 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: 2A10 FAB fragment light chain

H: 2A10 FAB fragment heavy chain

hetero molecules

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

2

B: 2A10 FAB fragment light chain

A: 2A10 FAB fragment heavy chain

hetero molecules

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

3

G: 2A10 FAB fragment light chain

I: 2A10 FAB fragment heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	231.684, 231.684, 81.784
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Antibody	2A10 FAB fragment light chain Mass: 23457.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody	2A10 FAB fragment heavy chain Mass: 23279.141 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.91 Å³/Da / Density % sol: 68.57 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0329 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0329 Å / Relative weight: 1
Reflection	Resolution: 3.01→39.733 Å / Num. obs: 44655 / % possible obs: 99.9 % / Redundancy: 14.6 % / Net I/σ(I): 10.6
Reflection shell	Resolution: 3.01→3.12 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 1.8 / CC_1/2: 0.703 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 3.011→39.733 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2467	2143	4.81 %
R_work	0.2248	-	-
obs	0.2259	44590	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.011→39.733 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9856	0	90	25	9971

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10177
X-RAY DIFFRACTION	f_angle_d	0.553	13849
X-RAY DIFFRACTION	f_dihedral_angle_d	10.369	3576
X-RAY DIFFRACTION	f_chiral_restr	0.021	1553
X-RAY DIFFRACTION	f_plane_restr	0.003	1741

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 (%)
3.0106-3.0806	0.3579	149	0.3522	2720	X-RAY DIFFRACTION	99
3.0806-3.1576	0.3903	130	0.3344	2840	X-RAY DIFFRACTION	100
3.1576-3.2429	0.3197	137	0.3157	2758	X-RAY DIFFRACTION	100
3.2429-3.3383	0.3149	151	0.3118	2776	X-RAY DIFFRACTION	100
3.3383-3.446	0.3055	158	0.2925	2787	X-RAY DIFFRACTION	100
3.446-3.5691	0.2804	130	0.282	2810	X-RAY DIFFRACTION	100
3.5691-3.7119	0.2842	129	0.2623	2825	X-RAY DIFFRACTION	100
3.7119-3.8807	0.2708	145	0.2393	2803	X-RAY DIFFRACTION	100
3.8807-4.0851	0.2454	144	0.2256	2811	X-RAY DIFFRACTION	100
4.0851-4.3407	0.2384	142	0.2057	2804	X-RAY DIFFRACTION	100
4.3407-4.6754	0.1936	144	0.1654	2829	X-RAY DIFFRACTION	100
4.6754-5.145	0.1763	136	0.1628	2871	X-RAY DIFFRACTION	100
5.145-5.8874	0.2049	136	0.1777	2876	X-RAY DIFFRACTION	100
5.8874-7.4097	0.1954	140	0.2098	2904	X-RAY DIFFRACTION	100
7.4097-39.7369	0.2269	172	0.1847	3033	X-RAY DIFFRACTION	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	8.344	-1.5981	4.3209	2.5129	-0.5344	7.373	-0.5115	1.2797	0.6573	-0.1702	0.09	-0.3726	-0.0864	1.5223	0.2912	0.402	0.0096	0.0667	0.6335	0.0344	0.4586	-65.3013	-21.557	-10.5874
2	4.1569	-1.6624	2.4615	2.3751	-0.4052	4.8755	-0.0341	0.689	-0.1309	-0.0558	0.0077	-0.1662	0.5626	0.7526	0.0127	0.44	0.1339	0.0411	0.5561	-0.0281	0.3571	-64.2265	-30.3697	-6.066
3	0.3592	0.5167	0.4383	1.3967	1.1581	2.1748	-0.4572	-0.033	0.0802	0.259	0.1967	-0.2776	0.248	0.7852	0.213	0.4739	0.0309	-0.024	0.5311	0.0669	0.3405	-89.084	-12.3634	-12.0206
4	3.718	-3.394	-2.4532	5.1629	3.6838	5.535	-0.0195	-0.0987	0.4626	-0.203	0.1501	-0.3459	-0.6856	0.2538	-0.1243	0.3977	-0.109	-0.0681	0.3635	0.0448	0.349	-92.7481	-3.3683	-4.6693
5	5.987	-1.6683	-0.8068	4.3253	0.7029	6.1372	-0.1649	-0.2361	-0.9637	0.2954	0.1674	0.6439	1.0073	0.568	-0.1888	0.4504	0.0599	-0.0346	0.4523	0.0407	0.3931	-73.6329	-34.9146	15.8648
6	3.0173	-0.9983	0.4752	5.1803	1.0164	4.8849	0.2236	0.4028	-0.3041	0.4267	-0.2026	0.0325	0.2139	0.5838	-0.0606	0.3795	0.1503	-0.0025	0.4205	-0.0329	0.444	-65.0458	-29.3901	11.8312
7	5.9591	-1.5618	-0.1746	2.0945	2.8548	4.0704	0.0728	-0.4265	0.2853	0.4546	0.296	-0.2737	-0.034	0.4014	-0.3519	0.5088	0.2203	0.0354	0.5313	-0.0835	0.4677	-63.727	-28.4456	18.761
8	5.9116	3.081	0.4034	6.4144	5.1688	4.6315	0.108	0.1686	0.6124	1.2893	0.0396	-0.2579	-0.1809	-0.2357	-0.2163	0.5123	0.211	-0.082	0.5659	0.0443	0.4087	-71.4565	-23.8878	19.6638
9	3.4495	-1.4742	-0.8782	3.3412	0.8448	1.6079	0.49	0.5597	-0.0951	-0.4503	-0.4635	-0.0821	0.4359	-0.5144	-0.0802	0.5725	0.1707	-0.0931	0.5554	0.0126	0.3347	-72.4684	-29.9704	9.5949
10	4.696	0.4697	1.8664	3.4625	0.908	8.0253	-0.1893	0.3164	0.1301	0.0793	0.0237	0.1486	-0.0876	0.0634	0.124	0.2942	-0.0245	0.064	0.2292	0.0346	0.3413	-96.9167	-15.5575	1.7649
11	4.3169	-2.3886	-0.822	2.7662	-0.3853	3.0254	0.254	0.1673	-0.7211	-0.3283	-0.0944	0.6746	0.3537	-0.0747	0.0245	0.411	-0.021	0.0668	0.3295	-0.0701	0.5531	-106.3641	-18.4485	-6.2649
12	9.2694	-1.6008	5.9883	6.8012	-4.1199	7.6051	-0.4319	-0.1663	0.1456	0.8607	0.0922	0.156	-0.3791	-1.0399	0.5038	0.6001	0.1593	0.106	0.5973	-0.0265	0.3537	-104.6053	-18.1095	6.4969
13	2.8727	-0.7118	3.4929	3.3832	-1.5887	8.118	0.1396	0.2742	-0.1547	-0.8056	-0.0379	-0.3502	0.3544	0.4378	-0.0931	0.4576	0.0348	0.1001	0.5572	-0.0793	0.4673	-91.6633	-31.5303	-38.1148
14	7.3018	-0.6146	0.5237	3.8259	-0.754	5.7031	0.1216	0.3417	0.5311	-0.0945	-0.1976	-0.2967	-0.6087	0.7292	0.0552	0.2749	-0.0183	0.0651	0.3292	0.0481	0.3797	-98.1474	-20.8111	-37.8524
15	4.9911	-0.1975	1.3997	1.2031	-3.0764	5.5616	-0.0277	0.5813	0.3456	-0.1707	-0.1362	-0.265	-0.203	0.6049	0.1046	0.3673	0.0191	0.066	0.3724	0.0026	0.3806	-96.1796	-25.4246	-38.8532
16	0.9827	0.7458	1.4946	5.3024	-3.2821	4.714	0.2467	0.1037	0.1499	-0.4718	-0.117	0.7823	0.4608	0.6031	-0.0894	0.3381	0.0161	0.0159	0.3514	-0.0659	0.4712	-88.9193	-43.2163	-15.4997
17	4.5861	2.003	-2.6949	6.2131	-3.9673	7.2443	0.3673	-0.2919	-0.2031	0.8927	0.1627	-0.0743	0.0477	-0.0589	-0.6713	0.5219	-0.0722	-0.0546	0.419	-0.0173	0.4078	-98.2078	-49.9959	-8.6676
18	4.1339	3.9716	-0.7902	5.1572	-0.707	3.4037	0.0365	0.1509	-1.0672	-0.1453	-0.1115	-0.6815	0.6605	-0.0555	0.0569	0.3933	0.0235	-0.0558	0.4759	-0.0867	0.6553	-94.3368	-54.3446	-14.1449
19	3.1918	-1.0982	1.1152	7.8652	-2.3176	6.3455	0.1501	-0.4824	0.2106	0.7054	0.0011	0.3225	-0.2441	-0.3417	-0.1343	0.2713	-0.028	0.0213	0.3463	-0.0493	0.2987	-117.256	-23.9999	-32.5371
20	5.2074	3.3641	3.089	8.8879	-2.2998	4.4053	0.2052	-0.1181	-0.3314	-0.9019	-0.0616	0.7045	0.6711	-0.6677	-0.1483	0.4666	-0.1717	-0.0104	0.5048	0.0198	0.4146	-121.6173	-28.0385	-39.0852
21	3.8398	0.5049	0.2877	8.502	-3.3993	3.6088	0.0398	-0.0807	-0.0825	-0.3931	-0.037	-0.0899	0.2032	-0.1785	0.0068	0.2557	0.0002	-0.008	0.4169	-0.0586	0.2248	-116.9291	-28.2683	-33.3153
22	1.4686	0.0888	-0.0067	3.2444	-2.3208	3.9407	0.0009	-0.0451	-0.1657	0.2814	-0.0512	-0.2421	0.0619	0.0388	0.0655	0.3073	-0.0412	0.0376	0.255	-0.0873	0.3778	-103.3635	-39.787	-8.7246
23	7.361	-2.0375	3.502	3.9033	1.234	4.7246	-0.1424	-0.7135	-0.338	0.7927	0.1644	-0.104	-0.047	-0.2527	-0.1685	0.5297	-0.1357	0.0804	0.4956	0	0.3578	-107.7448	-42.0266	0.9582
24	6.0192	-2.589	2.6976	5.9334	1.0279	7.7146	0.094	0.9568	1.5665	-0.1844	0.0829	-0.819	-0.8822	0.4933	-0.0845	0.5757	0.1	0.117	0.5591	0.1777	0.9028	-32.8231	-4.5723	-44.5741
25	5.3937	-2.7303	0.1863	5.7829	1.2802	1.6751	0.1675	-0.0788	0.1366	-0.0473	-0.019	-0.6747	0.0249	0.3384	-0.1521	0.4387	0.1603	0.0132	0.5541	0.0108	0.5647	-37.3626	-4.7064	-35.7211
26	1.5673	-1.1924	-0.4686	0.3317	0.4935	0.282	0.2245	-0.1703	0.4803	-0.4427	-0.0866	-0.3867	-0.2238	-0.1746	-0.0659	0.639	0.3122	-0.003	0.7231	-0.0093	0.6186	-29.4489	-27.1417	-56.1673
27	2.5013	1.0506	1.8614	1.728	1.5826	2.472	-0.1044	0.5575	0.4362	-0.2895	-0.1048	0.2859	-0.2547	0.1166	0.2101	0.6208	0.2796	-0.0457	0.7501	0.0945	0.6944	-37.2476	-29.6437	-64.835
28	2.678	1.898	1.5678	2.1636	0.2385	1.0839	-0.0964	-0.0318	-0.2628	-0.2753	0.2336	0.3216	-0.2218	0.5752	-0.03	0.7802	0.2675	0.2248	0.9537	-0.1423	0.9185	-29.9103	-33.6257	-71.3799
29	4.3379	0.3414	2.612	3.8922	2.7261	7.071	0.1952	-0.2457	-0.25	0.6795	-0.1191	0.3384	0.4734	0.0221	-0.0963	0.5977	0.1342	0.0865	0.4628	0.0455	0.5007	-58.3663	-16.371	-32.2161
30	1.5615	0.612	-0.7443	2.2297	2.2815	6.5232	0.4287	0.3414	0.3262	-0.2423	-0.1961	-0.3906	-0.2192	-0.8098	-0.2797	0.4203	0.2229	-0.0318	0.5119	0.0053	0.4982	-55.1142	-6.9285	-36.7857
31	4.1217	1.0317	-0.7544	6.5506	1.8439	6.0223	0.1286	0.0982	0.7011	-0.6994	-0.0142	0.6389	-0.1066	-0.2972	-0.1242	0.5141	0.2383	-0.0459	0.5073	-0.0676	0.5288	-62.185	-6.2239	-37.6813
32	1.0654	1.0168	1.3373	3.1283	1.9315	2.6069	0.0301	-0.0458	-0.1694	-0.1079	0.1988	-0.1696	-0.0548	0.1883	-0.2152	0.5828	0.2652	0.0643	0.6388	0.0041	0.5128	-55.8031	-13.9808	-39.1322
33	4.688	-0.2488	-1.1461	3.9547	-0.084	2.393	-0.1581	-0.009	-0.062	-0.2368	-0.0971	-0.5428	0.3547	0.404	0.2083	0.6236	0.3212	0.0003	0.6179	0.048	0.4977	-42.6385	-36.4707	-54.134
34	4.188	-0.0249	-1.9236	2.6256	0.8869	1.668	0.284	0.083	-0.9782	-0.1872	-0.3564	-0.2717	0.7442	0.3478	0.0427	0.8423	0.2831	-0.0905	0.5833	0.0165	0.6158	-39.7632	-45.1592	-52.4806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 26 through 102 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 103 through 121 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 122 through 212 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 1 through 33 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 34 through 57 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 58 through 76 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 77 through 91 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 92 through 121 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 122 through 183 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 184 through 203 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 204 through 219 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 25 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 26 through 61 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 62 through 102 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 103 through 121 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 122 through 141 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 142 through 212 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 1 through 57 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 58 through 76 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 77 through 103 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 104 through 203 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 204 through 219 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 1 through 25 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 26 through 102 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 103 through 121 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 122 through 201 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 202 through 212 )
29	X-RAY DIFFRACTION	29	chain 'I' and (resid 1 through 33 )
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 34 through 57 )
31	X-RAY DIFFRACTION	31	chain 'I' and (resid 58 through 76 )
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 77 through 121 )
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 122 through 183 )
34	X-RAY DIFFRACTION	34	chain 'I' and (resid 184 through 219 )

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