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- PDB-6wm9: Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound ... -

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Basic information

Entry
Database: PDB / ID: 6wm9
TitlePlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 237235
Components
  • 237235 Fab heavy chain
  • 237235 Fab light chain
  • Reticulocyte binding protein 2b
KeywordsCELL INVASION / invasion / plasmodium vivax / malaria / antibody complex
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 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: 2.45 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
DepositionApr 20, 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
B: 237235 Fab heavy chain
E: 237235 Fab heavy chain
C: 237235 Fab light chain
F: 237235 Fab light chain
D: Reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)170,5146
Polymers170,5146
Non-polymers00
Water10,070559
1
A: Reticulocyte binding protein 2b
B: 237235 Fab heavy chain
C: 237235 Fab light chain


Theoretical massNumber of molelcules
Total (without water)85,2573
Polymers85,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 237235 Fab heavy chain
F: 237235 Fab light chain
D: Reticulocyte binding protein 2b


Theoretical massNumber of molelcules
Total (without water)85,2573
Polymers85,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.900, 86.780, 90.770
Angle α, β, γ (deg.)91.620, 109.980, 99.880
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.: 2
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 237235 Fab heavy chain


Mass: 25096.031 Da / Num. of mol.: 2 / Fragment: human antibody Fab heavy chain
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 237235 Fab light chain


Mass: 23641.076 Da / Num. of mol.: 2 / Fragment: human antibody Fab light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M magnesium formate, 15% (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: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→42.464 Å / Num. obs: 62389 / % possible obs: 97.4 % / Redundancy: 3.32 % / Biso Wilson estimate: 35.923 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.179 / Χ2: 0.885 / Net I/σ(I): 7.37 / Num. measured all: 207150 / Scaling rejects: 9
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
2.45-2.513.3680.6191.8315332471145520.7240.73696.6
2.51-2.583.4020.5532.1415507466745580.7890.65797.7
2.58-2.663.3720.4882.4314596443443290.840.58197.6
2.66-2.743.3210.4252.8414121438142520.8790.50897.1
2.74-2.833.2810.383.2213634425341560.8960.45697.7
2.83-2.933.1810.3243.6812605409439620.9090.3996.8
2.93-3.043.0530.2574.4811476390637590.940.31296.2
3.04-3.163.2510.225.312049380837060.960.26497.3
3.16-3.33.1210.1956.1210983365935190.9640.23696.2
3.3-3.463.4270.1458.7511803351034440.9810.17398.1
3.46-3.653.4440.12410.411153329932380.9870.14798.2
3.65-3.873.4220.11311.410419311730450.9870.13497.7
3.87-4.143.4320.10612.739954297229000.9890.12597.6
4.14-4.473.3960.09214.59043272026630.9890.1197.9
4.47-4.93.3570.09214.928190249124400.9880.1198
4.9-5.483.1620.08813.997044230322280.9890.10696.7
5.48-6.333.2060.10312.366313200619690.9840.12498.2
6.33-7.753.4060.0914.015759171916910.9920.10798.4
7.75-10.963.6550.05521.114671129912780.9970.06498.4
10.96-42.4643.5690.0523.3424987237000.9960.05996.8

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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: 2.45→42.464 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 31.75
RfactorNum. reflection% reflection
Rfree0.2788 3118 5 %
Rwork0.2232 --
obs0.2259 62347 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.94 Å2 / Biso mean: 33.5318 Å2 / Biso min: 11.17 Å2
Refinement stepCycle: final / Resolution: 2.45→42.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11251 0 0 559 11810
Biso mean---32.05 -
Num. residues----1462
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.48830.41611390.3348264396
2.4883-2.52910.33991410.273266698
2.5291-2.57270.30891440.2666275198
2.5727-2.61950.37711410.2594266697
2.6195-2.66990.31611430.253271198
2.6699-2.72440.34041390.2668265697
2.7244-2.78360.33911410.2552267798
2.7836-2.84830.31381430.2529272497
2.8483-2.91950.33921410.2585267797
2.9195-2.99850.32111400.2505265397
2.9985-3.08670.34671420.2532270697
3.0867-3.18630.30451400.2463265797
3.1863-3.30010.27961410.244266496
3.3001-3.43220.3011420.2226270898
3.4322-3.58830.27681430.2128271898
3.5883-3.77740.26751430.2043271498
3.7774-4.01390.27891410.2017267498
4.0139-4.32350.23741440.1848274398
4.3235-4.75810.20411430.1764271998
4.7581-5.44540.21081400.1839265997
5.4454-6.85590.25131440.2229273398

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