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- PDB-7k76: Crystal structure of MAD2-6 IgG Fab in complex with PfCSP N-termi... -

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Basic information

Entry
Database: PDB / ID: 7k76
TitleCrystal structure of MAD2-6 IgG Fab in complex with PfCSP N-terminal peptide.
Components
  • Heavy chain of MAD2-6 IgG Fab
  • Light chain of MAD2-6 IgG 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: 2.14 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 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 4, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 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

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Assembly

Deposited unit
A: Heavy chain of MAD2-6 IgG Fab
B: Light chain of MAD2-6 IgG Fab
H: Heavy chain of MAD2-6 IgG Fab
L: Light chain of MAD2-6 IgG Fab
P: PfCSP N-terminal peptide P17


Theoretical massNumber of molelcules
Total (without water)96,6615
Polymers96,6615
Non-polymers00
Water7,116395
1
A: Heavy chain of MAD2-6 IgG Fab
B: Light chain of MAD2-6 IgG Fab
P: PfCSP N-terminal peptide P17


Theoretical massNumber of molelcules
Total (without water)49,2423
Polymers49,2423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-30 kcal/mol
Surface area19430 Å2
MethodPISA
2
H: Heavy chain of MAD2-6 IgG Fab
L: Light chain of MAD2-6 IgG Fab


Theoretical massNumber of molelcules
Total (without water)47,4192
Polymers47,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-25 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.390, 77.320, 181.150
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 IgG Fab


Mass: 24044.104 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 Light chain of MAD2-6 IgG Fab


Mass: 23374.865 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 PfCSP N-terminal peptide P17


Mass: 1823.274 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M NH4-sulfate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.14→77.32 Å / Num. obs: 54785 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4429 / CC1/2: 0.777 / Rpim(I) all: 0.216 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.14→71.113 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 2000 3.66 %
Rwork0.1841 --
obs0.1854 54704 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→71.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 0 395 6995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026875
X-RAY DIFFRACTIONf_angle_d0.5819414
X-RAY DIFFRACTIONf_dihedral_angle_d8.0195495
X-RAY DIFFRACTIONf_chiral_restr0.0431079
X-RAY DIFFRACTIONf_plane_restr0.0041208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.19250.29951400.23113704X-RAY DIFFRACTION100
2.1925-2.25180.27041410.21743703X-RAY DIFFRACTION100
2.2518-2.31810.26691420.2163737X-RAY DIFFRACTION100
2.3181-2.39290.26591400.21063698X-RAY DIFFRACTION100
2.3929-2.47840.26131420.2033739X-RAY DIFFRACTION100
2.4784-2.57760.21731420.19833725X-RAY DIFFRACTION100
2.5776-2.6950.27671400.20173717X-RAY DIFFRACTION100
2.695-2.83710.23561420.19483733X-RAY DIFFRACTION100
2.8371-3.01480.25661420.18373755X-RAY DIFFRACTION100
3.0148-3.24760.20241440.17783764X-RAY DIFFRACTION100
3.2476-3.57440.19911420.17393763X-RAY DIFFRACTION100
3.5744-4.09160.18291450.15913817X-RAY DIFFRACTION100
4.0916-5.15470.17431450.15383837X-RAY DIFFRACTION100
5.1547-71.1130.20631530.19924012X-RAY DIFFRACTION100

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