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- PDB-6wty: Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound ... -

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Basic information

Entry
Database: PDB / ID: 6wty
TitlePlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 253245
Components
  • 253245 Fab heavy chain
  • 253245 Fab light chain
  • reticulocyte binding protein 2b
KeywordsCELL INVASION / invasion / plasmodium vivax / malaria / antibody complex
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / Reticulocyte binding protein 2, putative
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.481 Å
AuthorsChan, L.J. / Dietrich, M.H. / Tham, W.H.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1160042 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1143187 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1154937 Australia
Wellcome Trust208693/Z/17/Z Australia
CitationJournal: Nat Commun / Year: 2021
Title: Naturally acquired blocking human monoclonal antibodies to Plasmodium vivax reticulocyte binding protein 2b.
Authors: Chan, L.J. / Gandhirajan, A. / Carias, L.L. / Dietrich, M.H. / Vadas, O. / Visentin, R. / Franca, C.T. / Menant, S. / Soldati-Favre, D. / Mueller, I. / King, C.L. / Tham, W.H.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: reticulocyte binding protein 2b
J: reticulocyte binding protein 2b
G: reticulocyte binding protein 2b
C: 253245 Fab light chain
B: 253245 Fab heavy chain
F: 253245 Fab light chain
H: 253245 Fab heavy chain
L: 253245 Fab light chain
A: reticulocyte binding protein 2b
K: 253245 Fab heavy chain
E: 253245 Fab heavy chain
I: 253245 Fab light chain


Theoretical massNumber of molelcules
Total (without water)342,63812
Polymers342,63812
Non-polymers00
Water0
1
D: reticulocyte binding protein 2b
F: 253245 Fab light chain
E: 253245 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)85,6603
Polymers85,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: reticulocyte binding protein 2b
L: 253245 Fab light chain
K: 253245 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)85,6603
Polymers85,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: reticulocyte binding protein 2b
H: 253245 Fab heavy chain
I: 253245 Fab light chain


Theoretical massNumber of molelcules
Total (without water)85,6603
Polymers85,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: 253245 Fab light chain
B: 253245 Fab heavy chain
A: reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)85,6603
Polymers85,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.559, 78.189, 312.080
Angle α, β, γ (deg.)90.000, 94.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
reticulocyte binding protein 2b


Mass: 36519.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_094255 / Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A5K736
#2: Antibody
253245 Fab light chain


Mass: 23470.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody
253245 Fab heavy chain


Mass: 25668.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M sodium dihydrogen phosphate pH 4.0, 16% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.48→48.795 Å / Num. obs: 43497 / % possible obs: 98.7 % / Redundancy: 5.388 % / Biso Wilson estimate: 60.59 Å2 / CC1/2: 0.85 / Rmerge(I) obs: 0.772 / Rrim(I) all: 0.857 / Χ2: 0.613 / Net I/σ(I): 2.54 / Num. measured all: 234345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.48-3.695.0592.8560.5333144703665510.1313.17993.1
3.69-3.945.6352.1330.8437325663466240.2532.35499.8
3.94-4.265.5871.2741.4634311615061410.5231.40999.9
4.26-4.665.4540.8482.1831044571156920.70.9499.7
4.66-5.25.1430.6542.6526573519151670.7180.73299.5
5.2-65.4550.6772.5224859456745570.7170.75399.8
6-7.325.6390.543.1221889388638820.7870.59799.9
7.32-10.245.1780.1937.4915917308030740.9750.21599.8
10.24-48.7955.1320.12510.99283183718090.9870.13998.5

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W53

5w53


Resolution: 3.481→48.701 Å / Cross valid method: THROUGHOUT / σ(F): 1498.83 / Phase error: 42.24 / Stereochemistry target values: TWIN_LSQ_F
Details: Pseudo-merohedral twinning was detected. Therefore the structure was refined in the presence of the twinning operator (h, -k, -h-l) yielding an associated twin fraction of 0.15.
RfactorNum. reflection% reflection
Rfree0.3011 2058 4.75 %
Rwork0.2619 41297 -
obs0.2666 43318 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.14 Å2 / Biso mean: 74.7432 Å2 / Biso min: 32.68 Å2
Refinement stepCycle: final / Resolution: 3.481→48.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19922 0 0 0 19922
Num. residues----2891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4848-3.57190.35211100.31272514262480
3.5719-3.66840.32671440.30082921306595
3.6684-3.77630.35841470.29732977312495
3.7763-3.89810.33411430.28622998314195
3.8981-4.03720.34151430.28362917306095
4.0372-4.19870.33611430.27662965310895
4.1987-4.38960.31361520.27272996314895
4.3896-4.62060.30921370.25472948308595
4.6206-4.90960.32211480.25422949309795
4.9096-5.28780.27981390.25272980311995
5.2878-5.81840.30041470.26933010315795
5.8184-6.65680.33011440.28072980312495
6.6568-8.37320.24511450.24093024316995
8.3732-39.02760.25381550.23313118327395

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