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- PDB-7rxp: Fab1512 in complex with the C-terminal alpha-TSR domain of P. fal... -

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Basic information

Entry
Database: PDB / ID: 7rxp
TitleFab1512 in complex with the C-terminal alpha-TSR domain of P. falciparum
Components
  • Circumsporozoite protein
  • Fab1512 heavy chain
  • Fab1512 light chain
KeywordsIMMUNE SYSTEM / Malaria / Antibody / Sporozoite / Circumsporozoite protein / alpha-TSR domain
Function / homology
Function and homology information


host cell surface binding / symbiont entry into host / entry into host cell by a symbiont-containing vacuole / heparan sulfate proteoglycan binding / 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: 1.761 Å
AuthorsPholcharee, T. / Oyen, D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: A novel CSP C-terminal epitope targeted by an antibody with protective activity against Plasmodium falciparum.
Authors: Beutler, N. / Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / MacGill, R.S. / Garcia, E. / Calla, J. / Parren, M. / Yang, L. / Volkmuth, W. / Locke, E. / Regules, J.A. / Dutta, S. / ...Authors: Beutler, N. / Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / MacGill, R.S. / Garcia, E. / Calla, J. / Parren, M. / Yang, L. / Volkmuth, W. / Locke, E. / Regules, J.A. / Dutta, S. / Emerling, D. / Early, A.M. / Neafsey, D.E. / Winzeler, E. / King, C.R. / Zavala, F. / Burton, D.R. / Wilson, I.A. / Rogers, T.F.
History
DepositionAug 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab1512 light chain
H: Fab1512 heavy chain
A: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)56,4983
Polymers56,4983
Non-polymers00
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-29 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.012, 84.149, 90.217
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 Fab1512 light chain


Mass: 23830.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab1512 heavy chain


Mass: 25085.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Circumsporozoite protein


Mass: 7582.599 Da / Num. of mol.: 1
Fragment: C-terminal alpha-TSR domain (UNP residues 309-375)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0304600 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7K740
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3000, 0.2 M sodium chloride, 0.1 M HEPES. pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03324 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 55594 / % possible obs: 99.8 % / Redundancy: 11.5 % / CC1/2: 0.96 / Rpim(I) all: 0.033 / Rsym value: 0.108 / Net I/σ(I): 24
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 2685 / CC1/2: 0.769 / Rpim(I) all: 0.357 / Rsym value: 0.901

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 1.761→31.397 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 2769 4.99 %
Rwork0.1767 --
obs0.1781 55495 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.761→31.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 0 528 4447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114094
X-RAY DIFFRACTIONf_angle_d1.0385578
X-RAY DIFFRACTIONf_dihedral_angle_d10.8183233
X-RAY DIFFRACTIONf_chiral_restr0.06627
X-RAY DIFFRACTIONf_plane_restr0.007723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.761-1.7910.4081340.34972440X-RAY DIFFRACTION93
1.791-1.82350.36371510.31072579X-RAY DIFFRACTION100
1.8235-1.85860.31051450.24542601X-RAY DIFFRACTION100
1.8586-1.89650.23551560.20742585X-RAY DIFFRACTION100
1.8965-1.93780.23371360.19362606X-RAY DIFFRACTION100
1.9378-1.98280.22271260.192633X-RAY DIFFRACTION100
1.9828-2.03240.22571240.19952640X-RAY DIFFRACTION100
2.0324-2.08740.22921480.18052606X-RAY DIFFRACTION100
2.0874-2.14880.23451260.16762655X-RAY DIFFRACTION100
2.1488-2.21810.22321230.17062623X-RAY DIFFRACTION100
2.2181-2.29740.20541350.17542629X-RAY DIFFRACTION100
2.2974-2.38930.22631190.17662651X-RAY DIFFRACTION100
2.3893-2.4980.19381120.16862661X-RAY DIFFRACTION100
2.498-2.62970.18511090.17672678X-RAY DIFFRACTION100
2.6297-2.79430.20981490.18462644X-RAY DIFFRACTION100
2.7943-3.00990.20361490.18022665X-RAY DIFFRACTION100
3.0099-3.31250.21491510.17692640X-RAY DIFFRACTION100
3.3125-3.79110.17821640.15642660X-RAY DIFFRACTION100
3.7911-4.77370.16231630.13822713X-RAY DIFFRACTION100
4.7737-31.3970.16631490.17212817X-RAY DIFFRACTION99

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