PDB-6wg1: Crystal structure of Fab399 in complex with NPNA6 peptide from ci...

ID or keywords:

Entry

Database: PDB / ID: 6wg1

Title

Crystal structure of Fab399 in complex with NPNA6 peptide from circumsporozoite protein

Components

Fab399 heavy chain
Fab399 light chain
NPNA6 peptide

Keywords

IMMUNE SYSTEM /

Malaria /

Sporozoite /

Circumsporozoite protein /

Antibody

Function / homology

Function and homology information

entry into host cell by a symbiont-containing vacuole / side of membrane /

cell surface /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.086 Å

Authors

Pholcharee, T. / Oyen, D. / Wilson, I.A.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum.
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / Richter King, C. / Zavala, F. / Wilson, I.A.

History

Deposition	Apr 4, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 3, 2021	Group: Database references / Category: citation / citation_author
Revision 1.2	Apr 3, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wg1.cif.gz	349.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6wg1.ent.gz	284 KB	Display	PDB format
PDBx/mmJSON format	6wg1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/6wg1 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wg1	HTTPS FTP

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Related structure data

Related structure data	6w00C 6w05C 6wfwC 6wfxC 6wfyC 6wfzC 6wg0C 6wg2C C: citing same article (ref.)
Similar structure data	6wfz-d 5otj-d 2e1r-d 5o9a-d 3kfc-d 1u60-4 6zh7-d 2av7-d 6u3i-d 2npf-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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

A: Fab399 heavy chain

B: Fab399 light chain

H: Fab399 heavy chain

L: Fab399 light chain

C: NPNA6 peptide

98.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	62.968, 85.901, 89.461
Angle α, β, γ (deg.)	90.00, 100.27, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Fab399 heavy chain Mass: 23677.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	Fab399 light chain Mass: 24288.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide	NPNA6 peptide Mass: 2420.450 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893*PLUS
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.47 Å³/Da / Density % sol: 50.17 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50% MPD, 0.2 M ammonium phosphate monobasic, 0.1 M Tris, pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2019
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03316 Å / Relative weight: 1
Reflection	Resolution: 2.086→50 Å / Num. obs: 49542 / % possible obs: 89.1 % / Redundancy: 2.4 % / CC_1/2: 0.901 / R_pim(I) all: 0.06 / R_sym value: 0.082 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.086→2.14 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1393 / CC_1/2: 0.715 / R_pim(I) all: 0.333 / R_sym value: 0.407 / % possible all: 51

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.086→44.014 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.11

	R_factor	Num. reflection	% reflection
R_free	0.246	2434	4.92 %
R_work	0.1967	-	-
obs	0.1991	49513	88.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.086→44.014 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6670	0	0	347	7017

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6835
X-RAY DIFFRACTION	f_angle_d	0.72	9330
X-RAY DIFFRACTION	f_dihedral_angle_d	13.323	4031
X-RAY DIFFRACTION	f_chiral_restr	0.049	1061
X-RAY DIFFRACTION	f_plane_restr	0.005	1203

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 (%)
2.086-2.1284	0.332	66	0.2567	1397	X-RAY DIFFRACTION	45
2.1284-2.1747	0.2846	79	0.2596	1874	X-RAY DIFFRACTION	60
2.1747-2.2252	0.2922	94	0.2479	2206	X-RAY DIFFRACTION	71
2.2252-2.2809	0.3103	165	0.2435	2525	X-RAY DIFFRACTION	82
2.2809-2.3426	0.2968	153	0.2381	2839	X-RAY DIFFRACTION	91
2.3426-2.4115	0.2529	164	0.2351	3011	X-RAY DIFFRACTION	97
2.4115-2.4893	0.2707	155	0.2288	3043	X-RAY DIFFRACTION	98
2.4893-2.5783	0.2767	166	0.2261	3037	X-RAY DIFFRACTION	98
2.5783-2.6815	0.2719	139	0.2245	3083	X-RAY DIFFRACTION	98
2.6815-2.8035	0.2821	159	0.2273	3025	X-RAY DIFFRACTION	97
2.8035-2.9513	0.3099	167	0.2266	3003	X-RAY DIFFRACTION	96
2.9513-3.1361	0.3027	151	0.2251	2879	X-RAY DIFFRACTION	92
3.1361-3.3782	0.2878	129	0.2093	2955	X-RAY DIFFRACTION	94
3.3782-3.718	0.2587	168	0.1855	3023	X-RAY DIFFRACTION	96
3.718-4.2556	0.2082	147	0.1642	3058	X-RAY DIFFRACTION	97
4.2556-5.3602	0.1634	144	0.1403	3019	X-RAY DIFFRACTION	96
5.3602-44.014	0.197	188	0.1749	3102	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	0.6209	0.079	0.1318	0.4161	-0.1455	0.1869	-0.1326	0.1897	-0.3339	-0.0203	0.0332	0.1472	0.2897	-0.387	-0.0002	0.2561	-0.0256	-0.0093	0.2399	-0.0233	0.2784	24.4705	2.0346	-6.9963
2	0.3103	-0.014	0.4826	0.7507	0.0417	0.5742	-0.0243	0.3961	-0.1156	-0.1047	0.0928	0.0077	-0.0805	-0.3006	-0.0004	0.2015	0.0003	-0.043	0.2573	-0.0292	0.2494	23.0039	13.2197	-7.6641
3	1.1813	-0.4093	-0.7307	0.332	0.5026	0.7862	0.0239	0.2175	-0.0298	-0.0243	-0.0489	0.0045	0.0372	-0.2536	-0.0001	0.1914	-0.0189	-0.0026	0.2433	0.0081	0.2513	24.2778	8.1803	-9.097
4	0.1982	-0.04	-0.2932	0.6124	0.1417	0.8437	-0.1566	-0.081	-0.2411	0.0894	0.1072	-0.0648	0.0634	-0.0228	-0	0.2975	-0.0376	-0.0035	0.22	-0.0978	0.3755	50.8756	-2.9498	-22.5895
5	0.181	-0.204	-0.1078	0.8232	1.0192	0.8879	0.0552	-0.1006	-0.2794	-0.0117	0.032	-0.0233	0.0726	-0.0816	-0.0001	0.2701	-0.0286	-0.0284	0.2355	-0.0248	0.3589	52.9115	-1.2094	-15.5565
6	0.5431	-0.1508	-0.3855	0.0419	0.1596	0.5972	0.371	-0.0949	-0.4019	-0.165	-0.136	-0.0166	0.5375	0.008	0.0074	0.3345	0.028	-0.0589	0.1935	-0.0314	0.4691	55.3313	-11.1237	-16.4437
7	1.7251	1.0639	0.4716	1.0545	-0.0066	1.418	0.0152	-0.2448	0.198	-0.0213	-0.0104	0.0526	-0.0155	-0.0294	0.0001	0.193	-0.0086	-0.0097	0.1618	-0.0494	0.2921	36.6943	24.3442	1.3493
8	0.2498	0.0027	0.0445	0.3849	0.043	0.21	0.0981	-0.0971	0.1417	-0.1011	0.0146	-0.0281	-0.1036	0.0745	0	0.191	-0.0047	-0.023	0.1897	-0.0142	0.2492	42.6685	20.3927	-3.3093
9	0.5856	0.3736	-0.2374	0.4377	0.1619	0.3857	-0.0804	0.0262	-0.1245	-0.0298	0.0162	-0.1396	0.0241	0.0709	0.0001	0.2447	-0.0005	0.0471	0.2342	-0.0613	0.293	61.6531	5.6684	-22.9149
10	0.1661	-0.1209	0.0828	0.1387	-0.0921	0.0897	0.0822	0.0293	-0.1919	-0.2531	-0.0348	0.0448	0.0347	0.4268	-0.0001	0.3996	-0.0217	0.0052	0.3579	-0.0766	0.3381	59.3353	12.2504	-29.3036
11	0.14	-0.1438	-0.0453	1.0178	0.3671	0.6635	0.1625	0.0173	-0.0541	-0.1737	0.0164	-0.1844	-0.2518	0.0765	-0.0001	0.2804	-0.0273	0.0459	0.2812	-0.0598	0.3002	63.9098	8.395	-22.9169
12	0.2363	0.3664	-0.0389	1.8087	-0.4453	1.4432	0.1391	-0.1621	0.0319	0.3431	-0.2122	-0.0775	-0.0706	0.0493	0.0003	0.2739	-0.0703	-0.0079	0.2816	-0.0286	0.1921	13.9886	12.1921	26.3966
13	0.5179	0.1701	0.8033	0.1365	0.0803	0.8783	-0.0258	0.0236	-0.2984	0.0269	0.2173	-0.4237	-0.5176	0.6936	-0.0045	0.4704	-0.1605	0.0044	0.602	-0.0514	0.2556	12.9932	-10.681	44.7696
14	0.376	0.408	0.4465	0.5055	0.0893	1.1035	0.1768	-0.1147	-0.0588	0.208	-0.0146	-0.2118	-0.1942	0.6474	0	0.401	-0.1256	-0.0551	0.6321	-0.0528	0.313	14.4111	-13.6748	45.3265
15	0.9047	0.6991	-0.0983	0.7861	-0.7747	1.3928	0.044	0.0322	0.0102	-0.0776	0.1189	0.1868	0.1448	-0.1888	-0.0001	0.2465	-0.0514	-0.013	0.2637	0.0161	0.2685	-2.4539	2.0384	15.6803
16	-0.049	0.2994	0.0095	0.2001	-0.2979	0.0796	-0.022	-0.0337	0.1184	0.0763	0.1586	0.3739	0.0163	-0.2199	-0	0.2856	-0.0435	0.0224	0.2529	0.0029	0.3031	-4.1129	-1.3761	20.0324
17	1.4458	0.3274	0.0007	1.4526	0.1454	0.893	0.2036	-0.2426	0.0047	0.4254	-0.0875	0.1238	-0.0254	0.0769	0.0028	0.4562	-0.1043	0.0506	0.3952	0.0139	0.2171	-1.0574	-17.9781	50.2098
18	0.0949	-0.0479	0.1245	0.0152	-0.0404	0.1033	0.2331	-0.1383	0.0409	0.2553	0.0575	0.4941	-0.3886	-0.1687	-0.0002	0.3893	0.0059	0.0382	0.521	0.047	0.4873	10.0804	21.7555	1.2304
19	0.0245	0.056	0.0206	0.1344	0.0704	0.0488	0.4644	-0.5049	1.1572	0.8671	0.1415	0.1781	-0.4799	-0.5821	0.0092	0.3818	0.1424	0.083	0.4376	0.001	0.4314	8.6221	19.6101	12.4411

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 109 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 145 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1546 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 214 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 113 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 114 through 150 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 151 through 163 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 164 through 213 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 1 through 119 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 120 through 170 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 171 through 213 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 1 through 66 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 67 through 113 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 114 through 214 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1 through 17 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 18 through 24 )

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