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- PDB-8rz2: PfRH5 bound to monoclonal antibody R5.034 -

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Basic information

Entry
Database: PDB / ID: 8rz2
TitlePfRH5 bound to monoclonal antibody R5.034
Components
  • R5.034 heavy chain
  • R5.034 light chain
  • Reticulocyte binding protein 5
KeywordsIMMUNE SYSTEM / Malaria / blood stage / synthetic vaccine immunogen / PfRH5
Function / homologyRh5 coiled-coil domain / Rh5 coiled-coil domain / Reticulocyte binding protein 5
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFarrell, B. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Embo Mol Med / Year: 2024
Title: Rational structure-guided design of a blood stage malaria vaccine immunogen presenting a single epitope from PfRH5.
Authors: Harrison, T.E. / Alam, N. / Farrell, B. / Quinkert, D. / Lias, A.M. / King, L.D.W. / Barfod, L.K. / Draper, S.J. / Campeotto, I. / Higgins, M.K.
History
DepositionFeb 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte binding protein 5
B: R5.034 heavy chain
C: R5.034 light chain


Theoretical massNumber of molelcules
Total (without water)115,4963
Polymers115,4963
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-25 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.754, 82.993, 118.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reticulocyte binding protein 5


Mass: 63128.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B2L3N7
#2: Antibody R5.034 heavy chain


Mass: 27391.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody R5.034 light chain


Mass: 24975.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→82.99 Å / Num. obs: 32741 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 3402 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→68.03 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.458 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.449 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 1556 4.76 %RANDOM
Rwork0.2552 ---
obs0.2574 32667 100 %-
Displacement parametersBiso max: 146.89 Å2 / Biso mean: 72.57 Å2 / Biso min: 43.93 Å2
Baniso -1Baniso -2Baniso -3
1--17.6777 Å20 Å20 Å2
2--0.9237 Å20 Å2
3---16.7539 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.4→68.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5585 0 0 65 5650
Biso mean---68.9 -
Num. residues----708
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1965SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes949HARMONIC5
X-RAY DIFFRACTIONt_it5715HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion756SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4608SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5715HARMONIC20.006
X-RAY DIFFRACTIONt_angle_deg7742HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion18.3
LS refinement shellResolution: 2.4→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3368 30 4.59 %
Rwork0.335 624 -
all0.3351 654 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: 11.5473 Å / Origin y: -21.2812 Å / Origin z: -27.9032 Å
111213212223313233
T0.0311 Å20.0612 Å2-0.0449 Å2--0.0714 Å2-0.028 Å2---0.0459 Å2
L0.0891 °20.1761 °20.161 °2-0.639 °20.8891 °2--2.5528 °2
S0.0302 Å °-0.0199 Å °-0.0578 Å °0.0126 Å °-0.1409 Å °0.0265 Å °-0.1275 Å °-0.1459 Å °0.1107 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A158 - 501
2X-RAY DIFFRACTION1{ *|* }B158 - 501
3X-RAY DIFFRACTION1{ *|* }C158 - 501
4X-RAY DIFFRACTION1{ *|* }D158 - 501

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