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- PDB-7ufq: Structure of PfCSP peptide 21 with antibody P3-43 -

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Basic information

Entry
Database: PDB / ID: 7ufq
TitleStructure of PfCSP peptide 21 with antibody P3-43
Components
  • P3-43 Fab Heavy chain
  • P3-43 Fab Light chain
  • PfCSP peptide 21
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite
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
: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 P3-43
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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: P3-43 Fab Heavy chain
A: PfCSP peptide 21
L: P3-43 Fab Light chain
B: P3-43 Fab Heavy chain
C: PfCSP peptide 21
D: P3-43 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0917
Polymers99,9996
Non-polymers921
Water2,072115
1
H: P3-43 Fab Heavy chain
A: PfCSP peptide 21
L: P3-43 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0924
Polymers50,0003
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-31 kcal/mol
Surface area19250 Å2
MethodPISA
2
B: P3-43 Fab Heavy chain
C: PfCSP peptide 21
D: P3-43 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)50,0003
Polymers50,0003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.482, 61.697, 89.604
Angle α, β, γ (deg.)90.000, 103.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody P3-43 Fab Heavy chain


Mass: 24207.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein/peptide PfCSP peptide 21


Mass: 1562.553 Da / Num. of mol.: 2 / Fragment: Junctional peptide 21 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P02893
#3: Antibody P3-43 Fab Light chain


Mass: 24229.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.99 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris hydrochloride pH 8.5, 2.25 M Ammonium hydrogen phosphate

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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: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→43.52 Å / Num. obs: 34697 / % possible obs: 97.45 % / Redundancy: 3.4 % / CC1/2: 0.984 / Net I/σ(I): 8.92
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 3381 / CC1/2: 0.587

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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: 2.3→43.52 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 1702 4.94 %
Rwork0.2153 32772 -
obs0.2189 34474 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.88 Å2 / Biso mean: 33.6841 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: final / Resolution: 2.3→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6910 0 14 115 7039
Biso mean--20 31.21 -
Num. residues----906
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.370.31571500.2582266997
2.37-2.440.34911380.2541271898
2.44-2.530.31671300.2567273998
2.53-2.630.34681290.2472275799
2.63-2.750.33321430.2554273998
2.75-2.90.30631540.2392274799
2.9-3.080.35321220.2342275598
3.08-3.320.30131200.2168271196
3.32-3.650.25561380.2019277099
3.65-4.180.25221470.1899276798
4.18-5.260.26591590.1746266895

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