PDB-6wg2: Crystal structure of Fab239 in complex with NPNA4 peptide from ci...

ID or keywords:

Entry

Database: PDB / ID: 6wg2

Title

Crystal structure of Fab239 in complex with NPNA4 peptide from circumsporozoite protein

Components

Fab239 heavy chain
Fab239 light chain
NPNA4 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: 2.534 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
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wg2.cif.gz	341.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6wg2.ent.gz	277.4 KB	Display	PDB format
PDBx/mmJSON format	6wg2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wg2_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	6wg2_full_validation.pdf.gz	450 KB	Display
Data in XML	6wg2_validation.xml.gz	31.1 KB	Display
Data in CIF	6wg2_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/6wg2 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wg2	HTTPS FTP

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Related structure data

Related structure data	6w00C 6w05C 6wfwC 6wfxC 6wfyC 6wfzC 6wg0C 6wg1C C: citing same article (ref.)
Similar structure data	6lb8-2 1osp-d 1nc4-d 5y4l-d 5gpp-d 3zhh-d 5drn-d 1i1a-d 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

H: Fab239 heavy chain

I: Fab239 heavy chain

L: Fab239 light chain

M: Fab239 light chain

P: NPNA4 peptide

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	82.166, 55.706, 115.732
Angle α, β, γ (deg.)	90.00, 98.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Fab239 heavy chain Mass: 24197.186 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	Fab239 light chain Mass: 23614.164 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	NPNA4 peptide Mass: 1627.654 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 Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.74 Å³/Da / Density % sol: 55.09 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000, 0.1 M HEPES, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2019
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.534→50 Å / Num. obs: 31852 / % possible obs: 91.9 % / Redundancy: 3.7 % / CC_1/2: 0.88 / R_pim(I) all: 0.082 / R_sym value: 0.145 / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.534→2.58 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1613 / CC_1/2: 0.521 / R_pim(I) all: 0.522 / R_sym value: 0.898 / % possible all: 93.6

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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: 2.534→32.805 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.19

	R_factor	Num. reflection	% reflection
R_free	0.2464	1591	5 %
R_work	0.1945	-	-
obs	0.1971	31821	91.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.534→32.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6590	0	0	106	6696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6753
X-RAY DIFFRACTION	f_angle_d	0.565	9220
X-RAY DIFFRACTION	f_dihedral_angle_d	14.25	3968
X-RAY DIFFRACTION	f_chiral_restr	0.043	1046
X-RAY DIFFRACTION	f_plane_restr	0.005	1188

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 (%)
2.534-2.6155	0.3442	140	0.2816	2587	X-RAY DIFFRACTION	87
2.6155-2.7089	0.367	158	0.2745	2681	X-RAY DIFFRACTION	91
2.7089-2.8173	0.3487	136	0.2541	2672	X-RAY DIFFRACTION	89
2.8173-2.9455	0.3114	144	0.2582	2761	X-RAY DIFFRACTION	93
2.9455-3.1007	0.2819	149	0.2404	2764	X-RAY DIFFRACTION	93
3.1007-3.2948	0.2576	147	0.2153	2837	X-RAY DIFFRACTION	94
3.2948-3.5489	0.2862	119	0.1964	2798	X-RAY DIFFRACTION	93
3.5489-3.9055	0.2321	164	0.1828	2668	X-RAY DIFFRACTION	90
3.9055-4.4694	0.1887	142	0.1583	2850	X-RAY DIFFRACTION	94
4.4694-5.6264	0.17	145	0.1444	2747	X-RAY DIFFRACTION	90
5.6264-32.805	0.2272	147	0.1676	2865	X-RAY DIFFRACTION	91

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	1.7433	0.7636	0.646	3.0723	-0.1008	3.5882	0.4952	-0.0776	0.1639	-0.6017	0.1179	0.5751	0.1891	-1.2302	-0.4833	0.364	0.0581	-0.0212	0.566	0.1682	0.3546	6.7981	5.0274	4.4016
2	2.3015	2	1.0793	2	-6.5522	0.5061	1.7246	-4.5201	1.7518	4.0916	-2.3225	-3.4828	0.5491	4.6616	0.5908	0.915	0.0234	-0.4305	1.2248	-0.0842	0.5984	-0.7974	2.74	0.5469
3	1.9772	-1.3598	-0.4862	2.821	-0.3705	1.7725	0.0799	0.0496	-0.2072	-0.1848	-0.1112	0.1941	0.3177	-0.0392	0.0497	0.2874	-0.039	0.0159	0.2348	-0.0574	0.209	29.1672	-13.674	9.8774
4	1.8036	-1.0019	0.66	2.2806	0.9969	2.4179	-0.0564	0.1719	0.0149	0.1824	0.0552	0.0165	0.0991	0.1369	-0.0338	0.3057	-0.0503	0.0597	0.2177	0.0217	0.225	31.4228	-13.4212	9.6024
5	0.8396	0.1054	0.1459	1.2888	0.2751	1.4183	0.1957	-0.1818	-0.0386	0.2056	0.0604	-0.0969	0.4675	-0.0086	-0.2574	0.726	0.0564	-0.0763	0.3626	0.003	0.4146	51.2727	-30.9955	34.1667
6	1.259	0.0497	-0.1428	2.8424	-0.262	3.514	-0.0084	0.1964	-0.0915	-0.066	0.1262	0.1832	-0.2158	-0.2499	-0.0621	0.202	0.0255	0.0248	0.2849	0.004	0.2377	3.1771	1.1005	18.3547
7	0.2664	-0.1546	0.0654	1.4166	1.7949	2.5067	0.001	0.0239	0.0837	0.1406	-0.1136	0.0651	0.1286	-0.151	0.1207	0.2805	-0.0038	0.0149	0.2477	0.0543	0.273	2.2558	14.3713	41.1932
8	1.4579	-0.2013	-0.9445	1.2893	-1.247	4.2921	-0.0459	-0.1205	0.0371	0.0686	-0.0852	-0.2839	0.0441	0.1732	0.0785	0.2972	-0.0784	-0.0357	0.2996	-0.0215	0.287	46.2574	2.0149	25.1021
9	1.5622	-0.2919	1.1388	1.1024	0.0777	4.2611	-0.051	-0.0514	-0.002	0.231	0.0599	-0.0937	-0.4256	0.1584	0.0011	0.3618	-0.0056	-0.0053	0.186	-0.0013	0.2541	37.6291	2.697	20.9372
10	1.2034	-0.6528	0.2502	1.8214	-0.2832	0.6561	0.0853	-0.1747	-0.3285	0.1669	0.2713	-0.4708	-0.0009	0.019	-0.3488	0.3824	-0.0046	-0.1229	0.3887	-0.068	0.4468	58.9615	-20.5745	35.4405
11	3.046	-2.8266	-1.865	3.2662	1.0848	1.7628	0.0025	-0.0064	0.052	-0.0509	0.0118	-0.037	-0.0709	0.2957	0.016	0.3341	0.0423	-0.0795	0.4369	-0.0529	0.2869	61.7611	-16.8297	32.6033
12	5.1455	-2.0428	-2.0787	1.9966	0.8151	1.4064	0.1807	0.2117	0.2255	0.1249	-0.189	-0.1987	-0.1168	0.175	0.1363	0.5209	0.0267	-0.1096	0.3587	-0.0104	0.3238	57.9447	-15.6964	31.1617
13	2.1699	-1.8071	-0.3416	2.7735	0.5287	1.8518	0.1813	0.0173	0.1027	-0.2419	-0.3068	-0.0239	0.0458	0.0638	0.1088	0.4807	0.0258	0.0863	0.4702	-0.0056	0.3507	69.4004	-21.9133	31.6637
14	1.8175	-0.4797	-0.4429	1.9776	1.4478	1.5089	0.0964	0.1272	0.2155	-0.0423	0.0172	-0.2928	-0.3293	0.0362	-0.1139	0.3891	0.0522	0.055	0.3351	0.0813	0.3009	10.9681	24.067	14.4019
15	0.5327	0.2451	0.7781	0.7463	0.6237	1.216	0.123	0.1366	0.2126	0.0785	0.0342	-0.3032	-0.2573	0.0036	-0.1363	0.3536	0.0471	0.0709	0.277	0.0912	0.2992	10.9314	24.07	21.1959
16	1.6137	-0.3731	1.0098	1.6449	-0.9121	2.9642	0.0661	0.0409	0.0487	0.0237	-0.0227	-0.1627	0.0171	0.27	-0.0078	0.3303	0.0176	0.0076	0.2812	-0.0315	0.3026	17.0859	24.5316	51.2418
17	8.554	-0.0004	-0.714	2.3145	-0.1619	2.2545	0.2845	0.1423	-0.3066	0.3685	0.1202	-0.1929	0.0002	-0.2335	-0.4434	0.3122	-0.0001	0.0327	0.1276	-0.0286	0.2441	30.2271	1.0366	3.1282
18	2.3396	-2.1658	-1.7307	2.1075	1.8478	1.8725	-0.0285	0.2979	-0.303	0.1305	-0.4139	0.1734	-0.2766	-0.142	0.3493	0.2194	0.0287	0.1394	0.1967	0.0557	0.4341	18.4691	0.7385	6.2209

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'P' and (resid 12 through 16 )
2	X-RAY DIFFRACTION	2	chain 'P' and (resid 17 through 17 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 1 through 60 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 61 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 215 )
6	X-RAY DIFFRACTION	6	chain 'I' and (resid 2 through 76 )
7	X-RAY DIFFRACTION	7	chain 'I' and (resid 77 through 215 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 1 through 18 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 19 through 103 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 104 through 129 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 130 through 151 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 152 through 175 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 176 through 213 )
14	X-RAY DIFFRACTION	14	chain 'M' and (resid 1 through 75 )
15	X-RAY DIFFRACTION	15	chain 'M' and (resid 76 through 114 )
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 115 through 213 )
17	X-RAY DIFFRACTION	17	chain 'P' and (resid 2 through 6 )
18	X-RAY DIFFRACTION	18	chain 'P' and (resid 7 through 11 )

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