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

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Basic information

Entry
Database: PDB / ID: 6wtv
TitlePlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 258259
Components
  • 258259 Fab heavy chain
  • 258259 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: 3.05 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
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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: reticulocyte binding protein 2b
C: 258259 Fab light chain
B: 258259 Fab heavy chain
G: reticulocyte binding protein 2b
H: 258259 Fab heavy chain
I: 258259 Fab light chain
J: reticulocyte binding protein 2b
K: 258259 Fab heavy chain
L: 258259 Fab light chain
E: 258259 Fab heavy chain
F: 258259 Fab light chain
D: reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)340,62712
Polymers340,62712
Non-polymers00
Water00
1
A: reticulocyte binding protein 2b
C: 258259 Fab light chain
B: 258259 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)85,1573
Polymers85,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: reticulocyte binding protein 2b
H: 258259 Fab heavy chain
I: 258259 Fab light chain


Theoretical massNumber of molelcules
Total (without water)85,1573
Polymers85,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
J: reticulocyte binding protein 2b
K: 258259 Fab heavy chain
L: 258259 Fab light chain


Theoretical massNumber of molelcules
Total (without water)85,1573
Polymers85,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: 258259 Fab heavy chain
F: 258259 Fab light chain
D: reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)85,1573
Polymers85,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.800, 98.654, 103.094
Angle α, β, γ (deg.)114.150, 105.000, 89.690
Int Tables number1
Space group name H-MP1

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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
258259 Fab light chain


Mass: 23412.787 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
258259 Fab heavy chain


Mass: 25224.189 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)
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: 295 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium nitrate, 18% (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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.05→49.166 Å / Num. obs: 60526 / % possible obs: 97.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 37.794 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.226 / Χ2: 0.882 / Net I/σ(I): 5.16 / Num. measured all: 151296
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
3.05-3.232.4690.5161.97235131003795240.6550.65594.9
3.23-3.452.3630.3562.821642937891590.8130.45397.7
3.45-3.732.4130.2573.9220682876685710.8910.32797.8
3.73-4.082.630.1955.1220905809579500.9450.24798.2
4.08-4.562.6310.1456.7518887730071790.9690.18298.3
4.56-5.252.5820.1377.0816391646563480.9690.17398.2
5.25-6.422.4140.1615.8212881544253350.9530.20598
6.42-92.5050.1028.4210377425141420.9860.12997.4
9-49.1662.5960.05814.876018241823180.9930.07395.9

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Processing

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

5w53


Resolution: 3.05→45.006 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 3023 5 %
Rwork0.2352 57458 -
obs0.2373 60481 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.45 Å2 / Biso mean: 40.4997 Å2 / Biso min: 10.94 Å2
Refinement stepCycle: final / Resolution: 3.05→45.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20978 0 0 0 20978
Num. residues----2804
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0501-3.09770.36041360.3098257996
3.0977-3.14850.30851380.2959262398
3.1485-3.20280.32731360.2883258898
3.2028-3.2610.33081390.2792263398
3.261-3.32370.33111390.2773264098
3.3237-3.39150.32091340.2696254398
3.3915-3.46520.31341370.2561260698
3.4652-3.54580.30261380.2466262698
3.5458-3.63440.29921390.2567264399
3.6344-3.73270.29861350.2347255898
3.7327-3.84240.27521380.2456263098
3.8424-3.96640.29881380.2299261999
3.9664-4.10810.25111390.23264799
4.1081-4.27240.24861380.2122261598
4.2724-4.46670.23111390.203264599
4.4667-4.7020.24051390.1928262898
4.702-4.99620.23871360.1999259899
4.9962-5.38140.23891380.2045261198
5.3814-5.92180.27821380.2373262499
5.9218-6.77630.25551380.254261698
6.7763-8.52790.28131370.2239261898

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