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

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Basic information

Entry
Database: PDB / ID: 7ufn
TitleStructure of PfCSP peptide 21 with antibody P3-21
Components
  • P3-21 Fab Heavy chain
  • P3-21 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.2 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 P3-21
Authors: Tripathi, P. / Kwong, P.D.
History
DepositionMar 22, 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 6, 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

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Assembly

Deposited unit
B: P3-21 Fab Heavy chain
C: P3-21 Fab Light chain
D: P3-21 Fab Light chain
A: P3-21 Fab Heavy chain
E: PfCSP peptide 21
F: PfCSP peptide 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,53811
Polymers100,0576
Non-polymers4805
Water55831
1
B: P3-21 Fab Heavy chain
C: P3-21 Fab Light chain
F: PfCSP peptide 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4137
Polymers50,0293
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-64 kcal/mol
Surface area19800 Å2
MethodPISA
2
D: P3-21 Fab Light chain
A: P3-21 Fab Heavy chain
E: PfCSP peptide 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1254
Polymers50,0293
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-50 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.694, 124.033, 103.635
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody P3-21 Fab Heavy chain


Mass: 24296.336 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: Antibody P3-21 Fab Light chain


Mass: 24169.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide PfCSP peptide 21


Mass: 1562.553 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P08307
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 5% isopropanol, 2 M Lithium sulfate, 0.1 M Magnesium sulfate, and 0.1 M sodium acetate trihydrate pH 4.5

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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: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→51.82 Å / Num. obs: 46287 / % possible obs: 99.82 % / Redundancy: 3.6 % / CC1/2: 0.98 / Net I/σ(I): 5.74
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 4700 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5M

6b5m


Resolution: 2.2→51.82 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 2448 5.22 %
Rwork0.1641 44474 -
obs0.1662 46287 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 24.8355 Å2 / Biso min: 9.93 Å2
Refinement stepCycle: final / Resolution: 2.2→51.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6891 0 25 31 6947
Biso mean--57.45 34.28 -
Num. residues----903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.240.18141500.11642608
2.24-2.290.15961560.11582632
2.29-2.350.18111590.11762527
2.35-2.410.18131560.12162618
2.41-2.470.17351280.12892645
2.47-2.540.20871800.14142546
2.54-2.630.18691550.13132640
2.63-2.720.20011300.13562577
2.72-2.830.21261260.1472673
2.83-2.960.20861310.15862592
2.96-3.110.21461380.1852609
3.11-3.310.22331360.21062644
3.31-3.560.31361460.2212593
3.56-3.920.19971430.18382640
3.92-4.490.17791220.15462652
4.49-5.650.1761470.14712612

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