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- PDB-7ufo: Structure of PfCSP peptide 21 with antibody P3-42 -

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Basic information

Entry
Database: PDB / ID: 7ufo
TitleStructure of PfCSP peptide 21 with antibody P3-42
Components
  • P3-42 Fab Heavy chain
  • P3-42 Fab Light chain
  • PfCSP peptide 21
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite
Function / homology
Function and homology information


side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTripathi, P. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure of PfCSP peptide 21 with antibody P3-42
Authors: Tripathi, P. / Kwong, P.D.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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
H: P3-42 Fab Heavy chain
L: P3-42 Fab Light chain
A: PfCSP peptide 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4137
Polymers50,0373
Non-polymers3764
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-56 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.505, 60.691, 86.502
Angle α, β, γ (deg.)90.000, 106.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-465-

HOH

21H-522-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide PfCSP peptide 21


Mass: 1562.553 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P08307

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Antibody , 2 types, 2 molecules HL

#1: Antibody P3-42 Fab Heavy chain


Mass: 24244.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody P3-42 Fab Light chain


Mass: 24229.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 300 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris hydrochloride pH 8.5, 2.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.43 Å / Num. obs: 42986 / % possible obs: 98.18 % / Redundancy: 3.5 % / CC1/2: 0.988 / Net I/σ(I): 7.51
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 4118 / CC1/2: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6b5m

6b5m


Resolution: 1.8→46.43 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 2208 5.14 %
Rwork0.1916 40740 -
obs0.1932 42948 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.16 Å2 / Biso mean: 21.8196 Å2 / Biso min: 6.37 Å2
Refinement stepCycle: final / Resolution: 1.8→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 14 296 3776
Biso mean--29.71 24.83 -
Num. residues----455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.840.32051350.2741234792
1.84-1.880.27751310.2423254899
1.88-1.930.31541500.2208254399
1.93-1.980.26231430.2127252599
1.98-2.040.22991410.2073257199
2.04-2.110.24041250.2059256699
2.11-2.180.22511450.1896254999
2.18-2.270.22441390.197257999
2.27-2.370.24161350.1947255099
2.37-2.50.22911370.2001255399
2.5-2.650.25121350.2002242193
2.65-2.860.21841320.20192595100
2.86-3.140.2521430.20232589100
3.14-3.60.20621320.17742598100
3.6-4.530.16011370.1547261399

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