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- PDB-7k75: Crystal structure of MAD2-6 IgA Fab in complex with PfCSP N-termi... -

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Basic information

Entry
Database: PDB / ID: 7k75
TitleCrystal structure of MAD2-6 IgA Fab in complex with PfCSP N-terminal peptide.
Components
  • Heavy chain of MAD2-6 IgA Fab
  • Light chain of MAD2-6 IgA Fab
  • PfCSP N-terminal peptide P17
KeywordsIMMUNE SYSTEM / Malaria / circumsporozoite protein / N-terminal domain / region I / antibody
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPholcharee, T. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Sci Transl Med / Year: 2021
Title: Functional human IgA targets a conserved site on malaria sporozoites.
Authors: Tan, J. / Cho, H. / Pholcharee, T. / Pereira, L.S. / Doumbo, S. / Doumtabe, D. / Flynn, B.J. / Schon, A. / Kanatani, S. / Aylor, S.O. / Oyen, D. / Vistein, R. / Wang, L. / Dillon, M. / ...Authors: Tan, J. / Cho, H. / Pholcharee, T. / Pereira, L.S. / Doumbo, S. / Doumtabe, D. / Flynn, B.J. / Schon, A. / Kanatani, S. / Aylor, S.O. / Oyen, D. / Vistein, R. / Wang, L. / Dillon, M. / Skinner, J. / Peterson, M. / Li, S. / Idris, A.H. / Molina-Cruz, A. / Zhao, M. / Olano, L.R. / Lee, P.J. / Roth, A. / Sinnis, P. / Barillas-Mury, C. / Kayentao, K. / Ongoiba, A. / Francica, J.R. / Traore, B. / Wilson, I.A. / Seder, R.A. / Crompton, P.D.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of MAD2-6 IgA Fab
B: Light chain of MAD2-6 IgA Fab
D: Light chain of MAD2-6 IgA Fab
C: Heavy chain of MAD2-6 IgA Fab
I: Heavy chain of MAD2-6 IgA Fab
J: Light chain of MAD2-6 IgA Fab
M: Heavy chain of MAD2-6 IgA Fab
N: Light chain of MAD2-6 IgA Fab
E: PfCSP N-terminal peptide P17
F: PfCSP N-terminal peptide P17


Theoretical massNumber of molelcules
Total (without water)192,27710
Polymers192,27710
Non-polymers00
Water6,287349
1
A: Heavy chain of MAD2-6 IgA Fab
B: Light chain of MAD2-6 IgA Fab


Theoretical massNumber of molelcules
Total (without water)47,5632
Polymers47,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-28 kcal/mol
Surface area18480 Å2
MethodPISA
2
D: Light chain of MAD2-6 IgA Fab
C: Heavy chain of MAD2-6 IgA Fab


Theoretical massNumber of molelcules
Total (without water)47,5632
Polymers47,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-28 kcal/mol
Surface area18500 Å2
MethodPISA
3
I: Heavy chain of MAD2-6 IgA Fab
J: Light chain of MAD2-6 IgA Fab
F: PfCSP N-terminal peptide P17


Theoretical massNumber of molelcules
Total (without water)48,5753
Polymers48,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-32 kcal/mol
Surface area18620 Å2
MethodPISA
4
M: Heavy chain of MAD2-6 IgA Fab
N: Light chain of MAD2-6 IgA Fab
E: PfCSP N-terminal peptide P17


Theoretical massNumber of molelcules
Total (without water)48,5753
Polymers48,5753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-32 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.136, 153.680, 193.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
Heavy chain of MAD2-6 IgA Fab


Mass: 24188.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
Light chain of MAD2-6 IgA Fab


Mass: 23374.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide PfCSP N-terminal peptide P17


Mass: 1012.334 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 40% PEG-300, 0.1M phosphate-citrate pH 4.2, final pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 75359 / % possible obs: 99 % / Redundancy: 5 % / Biso Wilson estimate: 42.1 Å2 / CC1/2: 0.905 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3252 / CC1/2: 0.557 / Rpim(I) all: 0.494 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.5→41.96 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 3735 4.97 %
Rwork0.1923 --
obs0.1945 75186 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13167 0 0 349 13516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313545
X-RAY DIFFRACTIONf_angle_d0.60918553
X-RAY DIFFRACTIONf_dihedral_angle_d5.3231886
X-RAY DIFFRACTIONf_chiral_restr0.0412136
X-RAY DIFFRACTIONf_plane_restr0.0062399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36591090.31942237X-RAY DIFFRACTION85
2.53-2.570.39941370.30672424X-RAY DIFFRACTION92
2.57-2.60.3541300.30012562X-RAY DIFFRACTION96
2.6-2.640.37161410.28252590X-RAY DIFFRACTION99
2.64-2.680.31511330.2752627X-RAY DIFFRACTION99
2.68-2.720.35381450.26632670X-RAY DIFFRACTION100
2.72-2.760.32241360.24952611X-RAY DIFFRACTION100
2.76-2.810.32091420.24482682X-RAY DIFFRACTION100
2.81-2.860.31291260.23332625X-RAY DIFFRACTION100
2.86-2.920.26291400.23532668X-RAY DIFFRACTION100
2.92-2.980.31211370.23552648X-RAY DIFFRACTION100
2.98-3.040.29751480.23582662X-RAY DIFFRACTION100
3.04-3.110.23851550.21962619X-RAY DIFFRACTION100
3.11-3.190.26811340.22062676X-RAY DIFFRACTION100
3.19-3.280.27231510.20982647X-RAY DIFFRACTION100
3.28-3.370.26191390.20962655X-RAY DIFFRACTION100
3.37-3.480.21871550.20322691X-RAY DIFFRACTION100
3.48-3.610.22821240.18492640X-RAY DIFFRACTION100
3.61-3.750.21571160.18422702X-RAY DIFFRACTION100
3.75-3.920.22231360.17042675X-RAY DIFFRACTION100
3.92-4.130.21331540.15632709X-RAY DIFFRACTION100
4.13-4.390.1731460.13822672X-RAY DIFFRACTION100
4.39-4.720.18521390.12882709X-RAY DIFFRACTION100
4.72-5.20.16791430.13312716X-RAY DIFFRACTION100
5.2-5.950.17121260.15942743X-RAY DIFFRACTION100
5.95-7.490.20861390.19132777X-RAY DIFFRACTION100
7.49-41.960.20221540.18392814X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0889-0.0123-0.06770.0376-0.00680.0282-0.0625-0.02320.0302-0.1154-0.0173-0.0157-0.10560.0397-00.26240.0012-0.03390.2876-0.00460.279856.6053-44.464611.3342
20.11320.05460.00190.04510.02890.11040.0224-0.0269-0.0726-0.0978-0.0063-0.00710.0437-0.005600.28240.0354-0.02190.26990.00310.280451.2023-46.738911.2274
30.2042-0.0138-0.00830.07820.04950.2306-0.1231-0.07040.0666-0.24780.07390.03760.13940.2295-00.32780.01410.080.3098-0.02090.328453.8059-21.3592-11.7191
40.01850.00890.0260.01-0.0040.02030.0651-0.06530.18930.03960.04710.1484-0.0359-0.235-00.27660.01370.00320.31730.01130.347430.4648-31.601113.6048
50.08850.01730.07730.04290.00060.0504-0.01190.02370.10020.06930.02340.0639-0.0882-0.0404-00.2710.02850.01080.29290.00920.251738.6278-33.413621.2527
60.0158-0.00710.02170.0085-0.01250.0166-0.002-0.05260.0295-0.03670.10990.0038-0.2088-0.0297-00.30020.07180.03380.2880.06810.302534.3428-25.32517.5312
70.0145-0.0097-0.00560.00070.00310.00940.10420.0242-0.1176-0.2099-0.03660.0497-0.063-0.15210.00010.19350.0348-0.00240.21920.00630.258339.0251-40.438916.7992
80.07670.01780.08130.0151-0.00720.0636-0.0765-0.00970.0085-0.04690.0626-0.0170.17830.046200.31330.03180.05460.27570.01250.189242.0736-19.5212-10.7811
90.00130.0115-0.01450.0207-0.02240.01850.0204-0.14230.0123-0.14570.16070.1189-0.14720.0301-0.00010.3406-0.0110.00390.32340.00110.275237.2238-20.2733-13.7744
100.0105-0.00340.00190.01790.00850.0092-0.07990.3296-0.0294-0.07290.11440.052-0.00760.026-0.00010.4601-0.0604-0.06280.39610.04440.362135.9786-25.9307-20.9271
110.0452-0.01230.00010.0865-0.03660.0041-0.24660.00430.0678-0.10970.0005-0.09620.14980.1688-0.00060.3153-0.05020.01990.37550.02580.263140.1342-21.3149-16.4691
120.01550.02590.00190.0071-0.00250.0057-0.09370.09140.1413-0.29530.02060.0378-0.0887-0.00680.00020.4475-0.00970.04450.38480.08290.281337.1477-12.9874-21.4319
130.1251-0.0978-0.02250.10110.03930.12360.0297-0.01130.069-0.06880.0127-0.05-0.1499-0.057-00.23710.0149-0.00560.23590.02810.271828.176321.35334.7771
140.0139-0.0228-0.0170.1020.02190.00550.0592-0.04250.02490.005-0.0130.1452-0.03670.087400.1603-0.0199-0.02030.2990.00270.37122.30716.85369.7701
150.04690.0134-0.04990.0245-0.03690.0473-0.0823-0.1097-0.08230.11610.02880.15780.0758-0.1738-00.26280.00390.05610.32010.02340.35381.4651-3.941715.2291
160.09810.0590.05220.05010.0520.0371-0.0199-0.02150.09560.16910.12780.26870.0181-0.095700.28070.00790.10130.34420.06510.4057-0.5441-2.394418.3056
170.0047-0.0064-0.00620.02660.01920.0093-0.002-0.0343-0.04520.03870.1299-0.13120.01340.016300.4313-0.0046-0.01790.32370.08440.336835.7211-5.58989.3624
180.0969-0.0180.02540.0521-0.0510.0340.0423-0.0077-0.0547-0.29560.04590.11390.008-0.022700.2842-0.02470.04010.2656-0.00040.319740.14874.2014.6514
190.0223-0.00950.0283-0.0009-0.00060.0235-0.1874-0.0801-0.1381-0.0193-0.0577-0.2998-0.01060.0114-00.330.00870.02730.3780.02610.378648.66564.6499.3368
200.0918-0.0737-0.13990.0920.07080.0756-0.0783-0.0956-0.0037-0.15280.0445-0.02460.15540.0979-00.2681-0.00310.00220.29670.02610.288637.0681.14597.5747
210.0566-0.00190.01810.0119-0.00690.02820.04360.21040.1477-0.0530.15430.1418-0.1158-0.1930.05140.20250.0799-0.03560.43640.15330.4638-1.3733-7.97976.6927
220.0133-0.0374-0.00930.025-0.00350.0162-0.0699-0.08050.0692-0.03160.04740.01950.0069-0.0032-00.2402-0.02370.00010.21580.02160.316812.6324-7.75248.3373
230.01240.00610.0057-0.0012-0.00480.00790.16420.1145-0.0377-0.0305-0.00680.09130.0249-0.05010.00030.33060.0407-0.01350.46050.03170.31337.4921-2.0282-2.4484
240.00040.00310.00290.011-0.00450.0076-0.0149-0.1170.07920.09850.00740.04870.04840.1276-0.00010.3705-0.00130.00870.36490.01850.420914.9014-6.274519.4769
250.00760.0030.00670.0502-0.03910.0108-0.14480.1184-0.0078-0.24010.07660.07820.0174-0.0255-00.2817-0.042-0.06440.3236-0.00250.31578.5349-10.81261.4033
260.0934-0.0234-0.09390.0470.07530.5548-0.26240.420.1608-0.31320.31250.45550.7635-0.03930.0810.6627-0.4969-0.30950.60360.10270.505634.259628.0995-24.4406
270.2705-0.02510.08460.4822-0.23950.6847-0.45480.42540.4085-0.62710.36810.65510.7191-0.2342-0.25680.1979-0.4761-0.33110.39480.1460.638934.348331.2742-19.533
280.0186-0.0071-0.00210.0025-0.01680.00070.25430.0712-0.0025-0.23790.00780.13810.13480.00750.00080.75620.0787-0.21080.6489-0.02010.605939.70658.2492-47.4841
290.1726-0.1787-0.19340.43940.37650.33350.27560.0243-0.0575-0.77980.06280.26210.2183-0.01940.15560.66230.051-0.33570.50610.06070.409738.54850.5424-44.3964
300.1309-0.01480.06120.22480.01750.0210.01980.02970.0212-0.14520.04150.14390.14370.047900.2517-0.0642-0.03060.28680.00990.301953.249840.5379-15.9329
310.0603-0.0299-0.01690.03680.04780.10490.18820.08180.0842-0.3573-0.11420.0177-0.01370.03430.00240.4270.0553-0.14810.43510.0550.393339.513766.0582-39.0888
320.0225-0.03980.05370.03120.0350.07570.05230.05420.14230.04090.0001-0.0608-0.67060.023200.6873-0.0110.07330.41320.01430.354343.5315-21.868340.8483
330.0079-0.0207-0.02530.014-0.0090.0272-0.022-0.03410.0150.0890.1002-0.1003-0.4282-0.0029-00.69190.04880.04430.41130.00370.308139.8103-22.18747.0803
340.00980.01680.03730.114-0.00290.02380.1234-0.17740.1155-0.42040.1687-0.1861-0.23010.06080.00010.68120.03670.04460.4348-0.09160.494537.358-10.786274.1834
350.10470.0814-0.07760.0411-0.02670.12490.1427-0.0021-0.15520.031-0.07480.0926-0.1478-0.020100.4005-0.0278-0.00350.35630.00840.264239.0469-41.855554.6199
360.0831-0.0291-0.08660.0805-0.03240.00990.10970.03360.12110.0710.00080.0038-0.0661-0.0236-00.4050.04530.03570.28270.00220.279232.3971-26.023864.638
370.03250.0843-0.04950.0657-0.06550.03380.11930.06960.0756-0.0670.02240.3354-0.10150.0568-00.59670.03220.02280.38330.00920.548122.4366-17.041477.9136
380.00110.00680.0033-0.00020.0010.0004-0.05860.0192-0.02260.039-0.04740.00860.0247-0.0288-00.3394-0.0308-0.01980.53540.04670.365447.5025-44.673834.7021
390.0060.0144-0.00330.0107-0.00430.0031-0.06120.07890.0283-0.06640.0421-0.0416-0.00180.08100.4048-0.06340.03970.3889-0.03660.290249.710820.3907-4.6143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 225 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 18 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 69 )
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 83 )
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 127 )
9X-RAY DIFFRACTION9chain 'B' and (resid 128 through 149 )
10X-RAY DIFFRACTION10chain 'B' and (resid 150 through 162 )
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 197 )
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 213 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 90 )
14X-RAY DIFFRACTION14chain 'D' and (resid 91 through 112 )
15X-RAY DIFFRACTION15chain 'D' and (resid 113 through 149 )
16X-RAY DIFFRACTION16chain 'D' and (resid 150 through 213 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 17 )
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 53 )
19X-RAY DIFFRACTION19chain 'C' and (resid 54 through 74 )
20X-RAY DIFFRACTION20chain 'C' and (resid 75 through 129 )
21X-RAY DIFFRACTION21chain 'C' and (resid 130 through 143 )
22X-RAY DIFFRACTION22chain 'C' and (resid 144 through 164 )
23X-RAY DIFFRACTION23chain 'C' and (resid 165 through 175 )
24X-RAY DIFFRACTION24chain 'C' and (resid 176 through 188 )
25X-RAY DIFFRACTION25chain 'C' and (resid 189 through 225 )
26X-RAY DIFFRACTION26chain 'I' and (resid 2 through 41 )
27X-RAY DIFFRACTION27chain 'I' and (resid 42 through 129 )
28X-RAY DIFFRACTION28chain 'I' and (resid 130 through 154 )
29X-RAY DIFFRACTION29chain 'I' and (resid 155 through 225 )
30X-RAY DIFFRACTION30chain 'J' and (resid 1 through 112 )
31X-RAY DIFFRACTION31chain 'J' and (resid 113 through 213 )
32X-RAY DIFFRACTION32chain 'M' and (resid 2 through 84 )
33X-RAY DIFFRACTION33chain 'M' and (resid 85 through 129 )
34X-RAY DIFFRACTION34chain 'M' and (resid 130 through 225 )
35X-RAY DIFFRACTION35chain 'N' and (resid 1 through 83 )
36X-RAY DIFFRACTION36chain 'N' and (resid 84 through 127 )
37X-RAY DIFFRACTION37chain 'N' and (resid 128 through 213 )
38X-RAY DIFFRACTION38chain 'E' and (resid 1 through 8 )
39X-RAY DIFFRACTION39chain 'F' and (resid 1 through 8 )

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