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- PDB-9n6u: Crystal structure of 18F25 malarial antibody -

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Basic information

Entry
Database: PDB / ID: 9n6u
TitleCrystal structure of 18F25 malarial antibody
Components
  • 18F25 Heavy Chain
  • 18F25 Kappa Chain
KeywordsIMMUNE SYSTEM / antibody / malaria
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYoo, R. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2025
Title: Cryo-EM structure of endogenous Pfs230:Pfs48/45 complex with six antibodies reveals mechanisms of malaria transmission-blocking activity
Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van ...Authors: Bekkering, E.T. / Yoo, R. / Hailemariam, S. / Heide, F. / Ivanochko, D. / Jackman, M. / Proellochs, N.I. / Stoter, R. / van Gemert, G.J. / Maeda, A. / Yuguchi, T. / Wanders, O.T. / van Daalen, R.C. / Inklaar, M.R. / Andrade, C.M. / Jansen, P.W. / Vermeulen, M. / Bousema, T. / Takashima, E. / Rubinstein, J.L. / Kooij, T.W. / Jore, M.M. / Julien, J.P.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 18F25 Heavy Chain
L: 18F25 Kappa Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4016
Polymers47,0162
Non-polymers3844
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-68 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.642, 81.796, 140.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody 18F25 Heavy Chain


Mass: 23486.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 18F25 Kappa Chain


Mass: 23530.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na2SO4 20 %w/v PEG 3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920194 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920194 Å / Relative weight: 1
ReflectionResolution: 1.103→35.196 Å / Num. obs: 365949 / % possible obs: 99.43 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.18 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.79
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 5231 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.19 Å / SU ML: 0.1532 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 2997 5.18 %
Rwork0.1879 54875 -
obs0.1892 57872 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 20 604 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583554
X-RAY DIFFRACTIONf_angle_d0.83314873
X-RAY DIFFRACTIONf_chiral_restr0.0549544
X-RAY DIFFRACTIONf_plane_restr0.0062624
X-RAY DIFFRACTIONf_dihedral_angle_d13.03771310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.29151430.25042564X-RAY DIFFRACTION98.58
1.63-1.660.21421340.2442561X-RAY DIFFRACTION98.83
1.66-1.690.25071520.23442524X-RAY DIFFRACTION99.07
1.69-1.720.261570.22792579X-RAY DIFFRACTION99.06
1.72-1.750.22541280.22662551X-RAY DIFFRACTION98.93
1.75-1.790.23731400.22482611X-RAY DIFFRACTION99.21
1.79-1.830.27681190.21782556X-RAY DIFFRACTION99.22
1.83-1.880.21681360.21112611X-RAY DIFFRACTION99.31
1.88-1.930.22051410.20312559X-RAY DIFFRACTION99.67
1.93-1.990.22251460.19522625X-RAY DIFFRACTION99.53
1.99-2.050.2131310.19582584X-RAY DIFFRACTION99.38
2.05-2.120.23561470.18962588X-RAY DIFFRACTION99.64
2.12-2.210.22871560.18882622X-RAY DIFFRACTION99.71
2.21-2.310.22451520.19252587X-RAY DIFFRACTION99.67
2.31-2.430.23131320.19842609X-RAY DIFFRACTION99.85
2.43-2.580.22891450.19412633X-RAY DIFFRACTION99.89
2.58-2.780.19561540.19192632X-RAY DIFFRACTION99.79
2.78-3.060.20241450.19182643X-RAY DIFFRACTION99.71
3.06-3.50.19631180.17162697X-RAY DIFFRACTION99.58
3.5-4.410.16721520.1542702X-RAY DIFFRACTION99.62
4.42-34.190.21411690.16332837X-RAY DIFFRACTION99.8

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