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- PDB-9dzc: PvRBP2b N-terminal domain stabilised mutant WHT2483 -

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Basic information

Entry
Database: PDB / ID: 9dzc
TitlePvRBP2b N-terminal domain stabilised mutant WHT2483
ComponentsReticulocyte-binding protein 2b
KeywordsCELL ADHESION / Malaria / Red Blood Cell / Reticulocyte Binding Protein
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / DI(HYDROXYETHYL)ETHER / Reticulocyte-binding protein 2b
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPymm, P. / D Sa, J. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2016908 Australia
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Stabilized designs of the malaria adhesin protein PvRBP2b for use as a potential diagnostic for Plasmodium vivax.
Authors: D Sa, J. / Krauss, L. / Smith, L. / D'Andrea, L. / Chan, L.J. / Abraham, A. / Kiernan-Walker, N. / Mazhari, R. / Lamont, M. / Lim, P.S. / Sattabongkot, J. / Lacerda, M.V. / Wini, L. / ...Authors: D Sa, J. / Krauss, L. / Smith, L. / D'Andrea, L. / Chan, L.J. / Abraham, A. / Kiernan-Walker, N. / Mazhari, R. / Lamont, M. / Lim, P.S. / Sattabongkot, J. / Lacerda, M.V. / Wini, L. / Mueller, I. / Longley, R.J. / Pymm, P. / Fleishman, S.J. / Tham, W.H.
History
DepositionOct 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reticulocyte-binding protein 2b
B: Reticulocyte-binding protein 2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09410
Polymers79,1442
Non-polymers9498
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.237, 92.828, 118.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Reticulocyte-binding protein 2b


Mass: 39572.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U4ERT5

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5 % MPD 10 % PEG 6000 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: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953647 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953647 Å / Relative weight: 1
ReflectionResolution: 2.4→47.38 Å / Num. obs: 34857 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 43.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.066 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3560 / CC1/2: 0.806 / Rpim(I) all: 0.425 / Χ2: 0.97 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.05 Å / SU ML: 0.2957 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 2000 5.75 %
Rwork0.1978 32760 -
obs0.2004 34760 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 62 177 5304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225270
X-RAY DIFFRACTIONf_angle_d0.44127087
X-RAY DIFFRACTIONf_chiral_restr0.0331763
X-RAY DIFFRACTIONf_plane_restr0.0024897
X-RAY DIFFRACTIONf_dihedral_angle_d15.57452048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.36821370.2732237X-RAY DIFFRACTION97.02
2.46-2.520.28141400.24112291X-RAY DIFFRACTION99.96
2.52-2.60.30631420.2452340X-RAY DIFFRACTION100
2.6-2.680.28121410.24182311X-RAY DIFFRACTION100
2.68-2.780.27341420.24532315X-RAY DIFFRACTION100
2.78-2.890.30121410.24212323X-RAY DIFFRACTION100
2.89-3.020.28091420.22252331X-RAY DIFFRACTION99.96
3.02-3.180.25661420.21982316X-RAY DIFFRACTION100
3.18-3.380.27911430.21372341X-RAY DIFFRACTION99.92
3.38-3.640.26271420.19872335X-RAY DIFFRACTION99.64
3.64-4.010.25331430.18322344X-RAY DIFFRACTION99.84
4.01-4.580.20441460.16412384X-RAY DIFFRACTION99.76
4.59-5.770.18711450.16782387X-RAY DIFFRACTION99.69
5.77-40.050.21711540.17772505X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 23.3306062458 Å / Origin y: 13.7958362553 Å / Origin z: 29.5577914105 Å
111213212223313233
T0.313540844493 Å2-0.0316935881134 Å2-0.00362375991287 Å2-0.226673349726 Å2-0.0116493769191 Å2--0.355181095399 Å2
L0.203367641898 °2-0.0689412532744 °2-0.29629132215 °2-0.167511860737 °20.243621213482 °2--1.46403984198 °2
S0.0233733038348 Å °-0.0165752484148 Å °0.00115730125246 Å °0.030743623436 Å °0.032857345749 Å °0.00637506228485 Å °0.0488102185728 Å °0.0172932982937 Å °-0.0507985313118 Å °
Refinement TLS groupSelection details: all

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