PDB-4kph: Structure of the Fab fragment of N62, a protective monoclonal ant...

ID or keywords:

Entry

Database: PDB / ID: 4kph

Title

Structure of the Fab fragment of N62, a protective monoclonal antibody to the nonreducing end of Francisella tularensis O-antigen

Components

N62 heavy chain
N62 light chain

Keywords

IMMUNE SYSTEM / antibody / immunoglobulin / Carbohydrate/Sugar Binding / plasma

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.59 Å

Authors

Lu, Z. / Rynkiewicz, M.J. / Yang, C.-Y. / Madico, G. / Perkins, H.M. / Wang, Q. / Costello, C.E. / Zaia, J. / Seaton, B.A. / Sharon, J.

Citation

Journal: Immunology / Year: 2013
Title: The binding sites of monoclonal antibodies to the non-reducing end of Francisella tularensis O-antigen accommodate mainly the terminal saccharide.
Authors: Lu, Z. / Rynkiewicz, M.J. / Yang, C.Y. / Madico, G. / Perkins, H.M. / Wang, Q. / Costello, C.E. / Zaia, J. / Seaton, B.A. / Sharon, J.

History

Deposition	May 13, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2013	Group: Database references
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Sep 20, 2023	Group: Data collection / Database references ...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 / 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
Revision 2.2	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4kph.cif.gz	318.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kp/4kph ftp://data.pdbj.org/pub/pdb/validation_reports/kp/4kph	HTTPS FTP

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Related structure data

Related structure data	3d9aS 3oz9S S: Starting model for refinement
Similar structure data	1bbj-2 5t1m-1 6wgb-1 4ong-d 6wgb-2 5f6i-d 4kq3-d 3ejy-4 5t78-2 6au5-2 5euk-2 1a0q-d 1jpt-d 3tnm-2 4jqi-2 1hxm-2 5f6h-4 6tul-d 5iop-2 6dez-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

3d9aS

3oz9S

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

L: N62 light chain

H: N62 heavy chain

M: N62 light chain

I: N62 heavy chain

hetero molecules

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

1

L: N62 light chain

H: N62 heavy chain

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

2

M: N62 light chain

I: N62 heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.874, 87.076, 153.589
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	N62 light chain Mass: 22950.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Fab fragment from cleavage of monoclonal antibody from cultured hybridoma cells Source: (natural) Mus musculus (house mouse) / Strain: BALB/cJ
#2: Antibody	N62 heavy chain Mass: 22961.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Fab fragment from cleavage of monoclonal antibody from cultured hybridoma cells Source: (natural) Mus musculus (house mouse) / Strain: BALB/cJ
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.51 Å³/Da / Density % sol: 50.95 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Microseeding by mixing 0.5 ul of Fab (12 mg/ml in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.02% NaN3) with 0.5 ul of reservoir solution [0.1 M bistris (pH 6.5), 0.2 M ammonium acetate, 25% w/v ...Details: Microseeding by mixing 0.5 ul of Fab (12 mg/ml in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.02% NaN3) with 0.5 ul of reservoir solution [0.1 M bistris (pH 6.5), 0.2 M ammonium acetate, 25% w/v PEG 3350] and streaking after equilibration, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal

Density Matthews: 2.51 Å³/Da / Density % sol: 50.95 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Microseeding by mixing 0.5 ul of Fab (12 mg/ml in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.02% NaN3) with 0.5 ul of reservoir solution [0.1 M bistris (pH 6.5), 0.2 M ammonium acetate, 25% w/v ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 18, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Redundancy: 3.8 % / Av σ(I) over netI: 20.85 / Number: 110303 / R_merge(I) obs: 0.068 / Χ²: 1.39 / D res high: 2.6 Å / D res low: 15 Å / Num. obs: 28828 / % possible obs: 98.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.52	15	97.6	1	0.033	1.383	3.7
4.42	5.52	99	1	0.039	1.196	3.9
3.87	4.42	99.4	1	0.05	1.399	4
3.52	3.87	99.2	1	0.067	1.455	4
3.27	3.52	99.3	1	0.087	1.405	3.9
3.08	3.27	99.2	1	0.117	1.427	3.9
2.93	3.08	98.9	1	0.153	1.407	3.8
2.8	2.93	99	1	0.194	1.426	3.8
2.69	2.8	98.6	1	0.246	1.375	3.7
2.6	2.69	98.1	1	0.325	1.402	3.7

Reflection

Resolution: 2.593→15 Å / Num. obs: 28828 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.068 / Net I/σ(I): 14.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.6-2.69	3.7	0.325	1	98.1
2.69-2.8	3.7	0.246	1	98.6
2.8-2.93	3.8	0.194	1	99
2.93-3.08	3.8	0.153	1	98.9
3.08-3.27	3.9	0.117	1	99.2
3.27-3.52	3.9	0.087	1	99.3
3.52-3.87	4	0.067	1	99.2
3.87-4.42	4	0.05	1	99.4
4.42-5.52	3.9	0.039	1	99
5.52-15	3.7	0.033	1	97.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.59 Å	14.87 Å
Translation	2.59 Å	14.87 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.5.0	phasing
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain)

3oz9

3d9a

Resolution: 2.59→14.87 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 0 / Phase error: 30 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.268	1946	6.94 %
R_work	0.222	-	-
obs	0.225	28036	96 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.59→14.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6220	0	4	31	6255

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6392
X-RAY DIFFRACTION	f_angle_d	0.666	8720
X-RAY DIFFRACTION	f_dihedral_angle_d	10.369	2243
X-RAY DIFFRACTION	f_chiral_restr	0.043	1000
X-RAY DIFFRACTION	f_plane_restr	0.004	1090

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 (%)
2.5928-2.6573	0.3464	122	0.2642	1666	X-RAY DIFFRACTION	87
2.6573-2.7287	0.3568	132	0.2752	1765	X-RAY DIFFRACTION	93
2.7287-2.8085	0.3339	132	0.2674	1793	X-RAY DIFFRACTION	94
2.8085-2.8985	0.2817	137	0.2656	1827	X-RAY DIFFRACTION	95
2.8985-3.0013	0.2812	137	0.2523	1823	X-RAY DIFFRACTION	95
3.0013-3.1204	0.313	135	0.2581	1841	X-RAY DIFFRACTION	97
3.1204-3.261	0.2853	139	0.2537	1864	X-RAY DIFFRACTION	97
3.261-3.4309	0.3566	141	0.2561	1872	X-RAY DIFFRACTION	98
3.4309-3.6429	0.2606	143	0.2366	1909	X-RAY DIFFRACTION	99
3.6429-3.9194	0.2664	143	0.2212	1908	X-RAY DIFFRACTION	98
3.9194-4.3051	0.2111	147	0.1988	1943	X-RAY DIFFRACTION	99
4.3051-4.9084	0.2172	143	0.1684	1918	X-RAY DIFFRACTION	99
4.9084-6.1117	0.2379	145	0.1886	1963	X-RAY DIFFRACTION	99
6.1117-14.8711	0.2683	150	0.2003	1998	X-RAY DIFFRACTION	97

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	0.1744	0.1009	0.0142	0.2738	-0.1234	0.0872	-0.0672	0.1589	-0.3198	-0.1173	-0.2115	0.1267	0.0956	-0.056	-0.697	0.3779	0.1619	0.0965	0.3169	-0.0629	0.3003	-5.2891	17.6723	-40.1893
2	0.1406	-0.2993	-0.2366	0.6196	0.4966	0.3943	0.306	0.2016	0.2341	-0.2925	-0.0785	-0.2952	-0.3881	0.0047	0.0269	0.2805	0.0411	0.0556	0.3452	0.0062	0.3301	-0.9754	28.4221	-35.9718
3	0.2753	0.7679	-0.1597	2.131	-0.3797	0.6511	0.055	0.3365	-0.2311	-0.3129	-0.2148	-0.7679	0.0003	0.369	0.0392	0.2998	0.0295	0.0868	0.4032	0.0246	0.3542	0.8868	25.2234	-38.5303
4	0.7674	0.0167	0.3296	0.5568	-0.6455	0.9164	0.1675	-0.1001	-0.256	-0.2169	-0.1208	-0.1119	0.2898	0.1168	0.7701	0.1613	0.0007	0.0327	0.126	-0.0078	0.2176	-13.6218	9.6254	-12.9516
5	0.3462	-0.116	-0.0345	0.8588	-0.3556	0.1674	0.0012	0.2826	-0.2276	-0.1053	-0.0437	0.1439	0.1882	-0.0477	0.0116	0.1655	-0.0246	0.0948	0.232	-0.0158	0.4658	-26.6579	2.6462	-9.9676
6	1.1809	-0.5847	1.0839	0.4056	-0.3589	1.2758	-0.072	-0.0182	-0.115	-0.0909	0.0236	-0.0993	-0.2009	-0.1855	0.4995	0.3973	0.0865	0.0234	0.1701	-0.0637	0.2892	-13.0108	11.9133	-19.0351
7	0.998	0.1189	-0.3368	0.3769	-0.6262	1.0638	-0.1846	0.0449	-0.5847	-0.0067	0.0008	0.2814	0.4861	-0.0849	0.1908	0.2366	-0.0678	0.0799	0.2936	0.052	0.3829	-22.6818	4.8826	-6.3699
8	0.6909	-0.5299	0.0892	2.1075	-0.2628	1.0558	-0.0712	-0.1404	0.3216	0.2082	0.0543	-0.7332	-0.4208	0.4429	-0.0059	0.2685	-0.0636	-0.0019	0.3278	-0.0043	0.3833	-4.4173	43.7453	-26.3485
9	0.1945	-0.0297	0.1091	0.6702	0.0685	0.5409	-0.0345	-0.1508	0.1246	0.1187	0.0589	-0.2076	-0.0329	0.1433	-0.001	0.1884	0.0342	0.0412	0.2757	0.042	0.1792	-10.2219	37.7925	-22.9282
10	0.4142	0.128	-0.0025	0.043	0.0118	0.2068	0.0538	0.039	-0.137	-0.0256	-0.0076	-0.1878	-0.0027	0.0793	-0.0766	0.0284	0.0313	-0.0122	0.2061	0.017	0.2632	-10.9459	19.512	-5.6001
11	0.1891	-0.0415	0.1017	0.2069	0.0299	0.2364	-0.1537	-0.2485	0.0684	0.0494	-0.0247	0.0331	0.0617	-0.2575	-0.0092	0.1791	0.0052	-0.0675	0.1933	0.0169	0.1637	-11.0218	19.0338	-12.7179
12	0.0381	0.0492	0.0697	0.0859	0.1452	0.2935	0.0358	-0.1523	-0.079	0.1721	-0.0102	-0.1482	0.1386	0.2814	-0.2585	-0.0562	0.0434	-0.2027	0.2771	0.1095	-0.0024	-7.5524	20.4908	-2.8126
13	0.3854	0.17	0.1247	0.089	-0.0131	0.4149	-0.0763	0.1131	-0.2344	-0.1518	0.0145	-0.0588	0.0599	0.0377	-0.4874	0.3648	0.0018	0.0132	0.0962	-0.056	0.2046	27.8356	-4.3772	-38.8264
14	0.9218	-0.8796	0.4636	1.0763	-0.5185	1.7336	0.2215	0.086	0.2481	-0.082	-0.0325	-0.4825	-0.2089	0.4592	-0.0623	0.3361	-0.0196	0.0057	0.1951	-0.0268	0.2669	35.8803	3.9025	-39.2398
15	1.1329	-0.1272	-0.3753	0.027	-0.0116	0.6739	-0.0522	0.055	-0.2546	0.0276	-0.0981	0.0924	0.1544	0.0191	-0.4013	0.3183	0.0056	-0.0228	0.1553	-0.0166	0.1188	29.9965	-0.8537	-33.4988
16	0.0839	-0.0646	0.0617	0.0501	-0.0483	0.0457	-0.0398	-0.1304	-0.1788	-0.0833	0.1247	0.1139	0.1625	-0.1615	0.4385	0.5821	-0.2152	0.2399	0.3984	0.0707	0.444	14.666	-8.5975	-2.4161
17	0.5674	-0.3543	-0.717	0.8837	0.7998	1.9093	0.0688	0.0741	-0.0222	-0.2067	-0.3382	0.278	0.3893	-0.5874	-0.0877	0.464	-0.1602	-0.0028	0.3371	0.031	0.3547	15.5473	-13.7612	-18.325
18	0.3452	-0.0183	-0.1276	0.5603	-0.0451	0.0798	-0.0445	-0.1121	-0.0919	0.1905	-0.0138	-0.1914	0.0111	0.1091	-0.0041	0.5749	0.0073	-0.0249	0.2343	0.0812	0.3511	28.5636	-9.89	-21.6879
19	0.1818	-0.1903	0.0413	0.2166	-0.1257	0.4658	0.0179	-0.2494	-0.1797	0.0796	0.0655	0.328	0.0989	-0.3359	-0.2281	0.6766	-0.2631	0.2679	0.6055	0.0535	0.6612	6.5564	-9.8368	-2.8538
20	0.2392	-0.0931	-0.0498	0.4326	0.1188	0.0549	-0.0198	0.0306	-0.1183	0.0389	-0.0253	0.2264	-0.02	-0.0343	0.2008	0.9169	-0.3379	0.0883	0.4276	-0.0931	0.5101	14.1541	-21.6611	-12.4057
21	0.4753	-0.2837	0.0398	0.9052	-0.0548	0.6336	-0.18	-0.1544	0.1499	0.3404	0.1732	-0.1302	-0.0597	0.1316	-0.0097	0.2658	0.0041	-0.1045	0.1718	-0.0363	0.3034	30.4443	22.1178	-26.6477
22	0.5528	0.1961	0.0107	0.1882	-0.1571	0.2806	-0.2793	0.0287	0.2578	0.2374	0.2642	-0.0099	0.0552	-0.0973	-0.019	0.3063	0.0031	-0.0149	0.2279	-0.0661	0.2681	27.4036	16.4771	-26.2661
23	0.6894	0.2087	0.1962	0.4705	0.856	1.6014	0.0911	0.067	-0.0782	0.2594	0.0803	0.06	0.2945	0.0213	0.2413	0.2818	-0.0244	0.0878	0.2181	0.0336	0.2876	19.71	1.0503	-8.5443
24	1.5636	0.3014	0.0509	1.3093	0.3773	2.008	0.0501	-0.2985	-0.2569	0.4623	-0.0473	-0.0371	0.6622	0.4513	0.4255	0.5683	0.028	0.0589	0.3214	0.0851	0.1937	29.1661	-3.2868	-0.3654
25	0.5555	0.02	0.0472	0.795	-0.1336	0.0271	-0.0051	-0.1724	-0.037	0.2335	0.1214	-0.0327	0.2726	0.1035	0.5042	0.2658	-0.0221	-0.0382	0.3123	0.0361	0.0427	24.9196	2.4177	1.7372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 26 through 48 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 49 through 102 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 103 through 144 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 145 through 155 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 156 through 174 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 175 through 212 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 2 through 80 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 81 through 119 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 120 through 157 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 158 through 173 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 174 through 212 )
13	X-RAY DIFFRACTION	13	chain 'M' and (resid 2 through 18 )
14	X-RAY DIFFRACTION	14	chain 'M' and (resid 19 through 75 )
15	X-RAY DIFFRACTION	15	chain 'M' and (resid 76 through 113 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 114 through 137 )
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 138 through 163 )
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 164 through 174 )
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 175 through 191 )
20	X-RAY DIFFRACTION	20	chain 'M' and (resid 192 through 210 )
21	X-RAY DIFFRACTION	21	chain 'I' and (resid 1 through 80 )
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 81 through 109 )
23	X-RAY DIFFRACTION	23	chain 'I' and (resid 110 through 184 )
24	X-RAY DIFFRACTION	24	chain 'I' and (resid 185 through 202 )
25	X-RAY DIFFRACTION	25	chain 'I' and (resid 203 through 212 )

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