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- PDB-8zs0: Plasmodium falciparum Nucleoplasmin (PfNPM) -

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Basic information

Entry
Database: PDB / ID: 8zs0
TitlePlasmodium falciparum Nucleoplasmin (PfNPM)
ComponentsNucleoplasmin-like domain-containing protein
KeywordsGENE REGULATION / Histone chaperone
Function / homologyNucleoplasmin-like domain / Nucleoplasmin-like domain / nucleolus / Nucleoplasmin-like domain-containing protein
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSaharan, K. / Vasudevan, D.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22660/2017 India
Department of Biotechnology (DBT, India)BT/INF/22/SP33046/2019 India
Science and Engineering Research Board (SERB)CRG/2023/002836 India
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structure-function studies of a nucleoplasmin isoform from Plasmodium falciparum.
Authors: Saharan, K. / Baral, S. / Gandhi, S. / Singh, A.K. / Ghosh, S. / Das, R. / Nagaraj, V.A. / Vasudevan, D.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoplasmin-like domain-containing protein
A: Nucleoplasmin-like domain-containing protein
C: Nucleoplasmin-like domain-containing protein
D: Nucleoplasmin-like domain-containing protein
E: Nucleoplasmin-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)60,5835
Polymers60,5835
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-33 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.349, 89.349, 113.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Nucleoplasmin-like domain-containing protein


Mass: 12116.637 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Alanine residue at the residue position 2 is added during the cloning.
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_0813300 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: C0H4U4
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate. 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.25→113.28 Å / Num. obs: 15903 / % possible obs: 99.9 % / Redundancy: 24.8 % / CC1/2: 0.991 / Net I/σ(I): 10.6
Reflection shellResolution: 3.25→3.51 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1726 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→45.7 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 423 4.89 %
Rwork0.2241 --
obs0.226 15903 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 0 0 3623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043718
X-RAY DIFFRACTIONf_angle_d0.8965047
X-RAY DIFFRACTIONf_dihedral_angle_d7.396496
X-RAY DIFFRACTIONf_chiral_restr0.056582
X-RAY DIFFRACTIONf_plane_restr0.004657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.450.3634900.35692561X-RAY DIFFRACTION100
3.45-3.720.33191380.28592522X-RAY DIFFRACTION100
3.72-4.090.2871540.24252497X-RAY DIFFRACTION100
4.1-4.690.23321380.21292527X-RAY DIFFRACTION100
4.69-5.90.23631320.19112482X-RAY DIFFRACTION100
5.9-45.70.24461260.19282536X-RAY DIFFRACTION100

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