PDB-6wfz: Crystal structure of Fab399 in complex with NPNA3 peptide from ci...

ID or keywords:

Entry

Database: PDB / ID: 6wfz

Title

Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein

Components

Fab399 heavy chain
Fab399 light chain
NPNA3 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: 1.84 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	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6wfz.cif.gz	358.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6wfz.ent.gz	291.6 KB	Display	PDB format
PDBx/mmJSON format	6wfz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wfz_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	6wfz_full_validation.pdf.gz	458 KB	Display
Data in XML	6wfz_validation.xml.gz	34.4 KB	Display
Data in CIF	6wfz_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wf/6wfz ftp://data.pdbj.org/pub/pdb/validation_reports/wf/6wfz	HTTPS FTP

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Related structure data

Related structure data	6w00C 6w05C 6wfwC 6wfxC 6wfyC 6wg0C 6wg1C 6wg2C C: citing same article (ref.)
Similar structure data	4wy7-d 6mqe-2 3fo9-2 2v17-d 5mhg-d 5uel-d 4xbg-1 2a6i-d 6x1s-4 4p3c-d 6peh-1 5fhb-d 4xce-3 6axl-2 1nd0-3 6cw3-1 5dd1-d 4xcn-2 3tcl-2 6obd-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

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

A: Fab399 heavy chain

B: Fab399 light chain

C: NPNA3 peptide

H: Fab399 heavy chain

L: Fab399 light chain

P: NPNA3 peptide

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

1

A: Fab399 heavy chain

B: Fab399 light chain

C: NPNA3 peptide

defined by author
Evidence: gel filtration
49.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Fab399 heavy chain

L: Fab399 light chain

P: NPNA3 peptide

defined by author
49.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.395, 87.604, 89.645
Angle α, β, γ (deg.)	90.00, 101.06, 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	NPNA3 peptide Mass: 1231.255 Da / Num. of mol.: 2 / 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.: 367 / 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: 2.53 Å³/Da / Density % sol: 51.45 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 20% PEG 3350, 0.2 M potassium fluoride, pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03324 Å / Relative weight: 1
Reflection	Resolution: 1.84→50 Å / Num. obs: 80717 / % possible obs: 97.2 % / Redundancy: 3 % / CC_1/2: 0.917 / R_pim(I) all: 0.052 / R_sym value: 0.079 / Net I/σ(I): 18.6
Reflection shell	Resolution: 1.84→1.88 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3088 / CC_1/2: 0.692 / R_pim(I) all: 0.38 / R_sym value: 0.484 / % possible all: 74.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.16_3549: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 1.84→46.747 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.69

	R_factor	Num. reflection	% reflection
R_free	0.2245	3869	4.8 %
R_work	0.1857	-	-
obs	0.1876	80521	96.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.84→46.747 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6721	0	0	367	7088

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6969
X-RAY DIFFRACTION	f_angle_d	0.831	9508
X-RAY DIFFRACTION	f_dihedral_angle_d	12.087	5565
X-RAY DIFFRACTION	f_chiral_restr	0.055	1074
X-RAY DIFFRACTION	f_plane_restr	0.005	1233

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 (%)
1.84-1.8624	0.3709	103	0.3109	1716	X-RAY DIFFRACTION	61
1.8624-1.886	0.3626	119	0.2947	2162	X-RAY DIFFRACTION	79
1.886-1.9108	0.3086	111	0.2817	2495	X-RAY DIFFRACTION	87
1.9108-1.937	0.3098	146	0.2587	2601	X-RAY DIFFRACTION	93
1.937-1.9647	0.2783	123	0.2364	2696	X-RAY DIFFRACTION	96
1.9647-1.994	0.2868	130	0.2309	2789	X-RAY DIFFRACTION	97
1.994-2.0252	0.264	141	0.2213	2747	X-RAY DIFFRACTION	98
2.0252-2.0584	0.3024	136	0.224	2790	X-RAY DIFFRACTION	99
2.0584-2.0939	0.2888	128	0.2225	2815	X-RAY DIFFRACTION	99
2.0939-2.1319	0.2287	144	0.2216	2813	X-RAY DIFFRACTION	99
2.1319-2.173	0.2602	147	0.208	2818	X-RAY DIFFRACTION	100
2.173-2.2173	0.2639	126	0.2135	2803	X-RAY DIFFRACTION	100
2.2173-2.2655	0.2473	151	0.2002	2844	X-RAY DIFFRACTION	100
2.2655-2.3182	0.2403	153	0.1951	2811	X-RAY DIFFRACTION	100
2.3182-2.3762	0.2498	138	0.2045	2813	X-RAY DIFFRACTION	100
2.3762-2.4404	0.2708	148	0.2082	2857	X-RAY DIFFRACTION	100
2.4404-2.5122	0.2732	153	0.2193	2788	X-RAY DIFFRACTION	100
2.5122-2.5933	0.2851	138	0.2176	2843	X-RAY DIFFRACTION	100
2.5933-2.686	0.2659	154	0.2029	2804	X-RAY DIFFRACTION	100
2.686-2.7935	0.2362	136	0.2086	2835	X-RAY DIFFRACTION	100
2.7935-2.9207	0.2339	149	0.2146	2855	X-RAY DIFFRACTION	100
2.9207-3.0746	0.2514	148	0.2084	2820	X-RAY DIFFRACTION	100
3.0746-3.2672	0.2388	142	0.1998	2825	X-RAY DIFFRACTION	100
3.2672-3.5194	0.209	131	0.1868	2872	X-RAY DIFFRACTION	100
3.5194-3.8734	0.2167	159	0.1718	2818	X-RAY DIFFRACTION	100
3.8734-4.4335	0.1619	131	0.1415	2846	X-RAY DIFFRACTION	99
4.4335-5.5843	0.1636	130	0.128	2859	X-RAY DIFFRACTION	99
5.5843-46.747	0.1709	154	0.1552	2917	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	1.3129	-0.1577	-0.8846	1.1229	-0.1401	0.5947	-0.234	0.6692	-0.42	-0.036	0.0227	0.0295	0.1512	-0.4744	0.2049	0.207	-0.1358	0.0272	0.4814	-0.2036	0.3095	23.957	7.6647	-9.7383
2	0.4387	0.0986	-0.1987	0.6208	1.0788	1.3657	-0.4858	-0.2333	-0.8396	0.0258	-0.1711	-0.2533	0.3891	-0.3643	-0.5016	0.3775	-0.0695	0.1914	0.2506	0.1544	0.7241	54.1516	-3.7595	-16.4532
3	1.6317	0.3979	-0.0742	0.9009	0.0668	1.0518	0.0383	-0.0459	0.1117	0.1989	-0.0208	0.0128	-0.1463	-0.0926	0	0.2409	-0.0332	-0.0276	0.2203	-0.0014	0.2578	35.6494	24.5659	2.0263
4	0.8059	0.4748	-0.8422	-0.0903	-0.3877	0.6707	-0.0884	-0.0825	-0.3032	0.005	-0.0944	-0.056	0.008	0.0124	-0.0662	0.2276	-0.0327	-0.027	0.2615	0.0071	0.3224	47.0421	14.8881	-9.0313
5	0.2692	0.3892	-0.0009	0.4422	0.3676	0.2817	-0.0895	-0.0946	-0.235	-0.0833	-0.2495	-0.065	0.0534	-0.0828	0.0003	0.2509	0.0177	0.0213	0.2898	0.0569	0.3183	59.218	11.9906	-18.7797
6	0.4924	0.5403	-0.4027	0.524	-0.1393	0.7785	-0.0387	-0.2544	-0.3461	-0.1787	-0.3436	-0.4374	0.05	0.0974	-0.0809	0.2762	0.0759	0.1225	0.2333	0.0802	0.4274	65.9758	7.9459	-27.6292
7	-0.0045	-0.0173	-0.0135	0.0384	-0.0067	0.0059	0.1894	0.4769	0	-0.158	0.2029	0.8952	-0.1586	-0.2253	0.0002	0.3011	0.006	-0.0318	0.4332	0.0418	0.3985	12.7266	21.3611	-1.6839
8	0.2112	0.1498	-0.03	0.3671	0.0324	0.6121	0.1315	-0.1569	-0.1196	0.2089	-0.2985	-0.3967	-0.0972	0.3386	-0.0693	0.5006	-0.0931	-0.0597	0.3868	-0.0379	0.2934	16.0756	8.6796	34.3116
9	0.1021	-0.1311	-0.0049	0.3753	-0.1943	0.315	0.1127	-0.0735	0.019	-0.0587	-0.3258	-0.3177	0.0664	0.2391	-0.0337	0.2151	-0.0626	-0.0151	0.2994	-0.0144	0.2623	19.9938	9.7218	21.1306
10	0.4346	-0.056	0.4401	0.3441	0.212	0.4072	0.1607	-0.1433	0.08	0.1661	-0.0782	-0.0444	-0.0883	-0.1126	0.0001	0.2916	-0.0224	0.0094	0.202	-0.0274	0.2164	8.8139	14.1303	23.3349
11	0.1686	0.0933	0.144	0.1226	0.0338	0.1957	-0.1696	0.2636	0.0025	0.4994	0.0704	0.0037	-0.4251	0.2513	-0.0035	0.4783	-0.0362	0.0107	0.2758	-0.0449	0.2576	11.3124	19.5465	28.2393
12	0.167	-0.0871	0.1628	0.19	-0.1162	0.1981	0.0797	0.2034	-0.0157	0.4872	-0.2232	-0.1011	-0.1407	0.0812	-0.0022	0.4469	-0.1002	-0.0171	0.3394	-0.0244	0.2895	15.0725	14.9631	31.8768
13	0.1934	0.0732	0.005	0.1673	-0.0034	0.1153	0.0301	0.0579	-0.0202	0.0294	-0.0201	-0.1738	0.1292	0.2306	-0.0081	0.2485	-0.0478	-0.0249	0.2082	-0.0206	0.2068	10.5185	5.9618	21.5535
14	0.1965	0.0404	-0.1976	0.0086	-0.0105	0.4432	-0.1232	-0.136	-0.0811	-0.3651	0.2122	-0.2723	-0.1469	0.4613	-0.0102	0.432	-0.0197	-0.053	0.3781	-0.0457	0.3265	11.8342	-6.1397	49.3442
15	-0.0231	0.0644	-0.0571	0.0805	-0.1325	0.1685	0.0703	-0.1056	-0.0047	-0.0028	0.0126	-0.353	-0.2782	0.4153	-0.0081	0.3049	-0.0042	-0.0105	0.3062	-0.0203	0.3014	9.9304	-14.2868	47.3174
16	0.1271	0.1789	0.2661	0.4394	-0.2512	0.5499	-0.2248	-0.0965	-0.0577	-0.0872	0.2869	-0.0688	-0.1037	0.5973	0.0005	0.2842	-0.0267	0.005	0.3657	-0.0508	0.2655	10.1898	-12.1392	42.1866
17	0.193	0.0488	-0.0042	0.0115	-0.025	0.4198	-0.1152	-0.1516	-0.171	-0.1465	0.0988	-0.6143	-0.042	1.1367	-0.0062	0.3226	-0.0022	-0.0224	0.5895	-0.0372	0.4538	19.2239	-15.1906	45.4243
18	0.7186	0.6095	-0.7182	1.0427	-1.2543	1.2287	-0.1086	0.1321	0.0811	-0.1023	0.2309	0.1397	0.1608	-0.2466	0	0.2669	-0.0518	-0.0333	0.2239	0.0126	0.2213	-4.1974	0.2046	17.3869
19	0.7526	0.866	0.5363	1.2787	0.7412	0.6671	0.0879	-0.2712	0.0379	0.1862	-0.1156	0.0192	0.1089	-0.2382	-0.0001	0.3338	-0.0264	0.0138	0.2815	0.0031	0.2253	-1.7061	-18.3486	50.0326
20	-0.0041	0.0161	0.0209	0.0105	0.0316	0.0441	0.2873	0.2117	0.4738	0.386	0.0926	0.2115	-0.7882	-0.1595	0.0005	0.4293	0.06	0.0795	0.251	-0.0112	0.3472	7.3957	21.9248	12.1802

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 119 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 213 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 80 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 81 through 128 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 129 through 174 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 175 through 214 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 11 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 1 through 17 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 18 through 33 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 34 through 62 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 63 through 71 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 72 through 85 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 86 through 109 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 110 through 134 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 135 through 145 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 146 through 188 )
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 189 through 213 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 1 through 118 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 119 through 213 )
20	X-RAY DIFFRACTION	20	chain 'P' and (resid 1 through 11 )

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