5X7V

Crystal structure of Nucleosome assembly protein S (PfNapS) from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb5X7V/pdb
• Entry: 5X7V supersedes: 3KYP

• Classification: CHAPERONE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-27 Released: 2017-03-15 
• Deposition Author(s): Gill, J., Yogavel, M., Sharma, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.312 
• R-Value Work: 0.243 
• R-Value Observed: 0.247 

Literature

Structure, localization and histone binding properties of nuclear-associated nucleosome assembly protein from Plasmodium falciparum.

Gill, J., Kumar, A., Yogavel, M., Belrhali, H., Jain, S.K., Rug, M., Brown, M., Maier, A.G., Sharma, A.

(2010) Malar J 9: 90-90

• PubMed: 20377878 
• DOI: https://doi.org/10.1186/1475-2875-9-90
• Primary Citation of Related Structures:  
  5X7V


• PubMed Abstract: 
  

  Nucleosome assembly proteins (NAPs) are histone chaperones that are crucial for the shuttling and incorporation of histones into nucleosomes. NAPs participate in the assembly and disassembly of nucleosomes thus contributing to chromatin structure organization. The human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS.

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Organizational Affiliation: 

Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi, 110067, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137.96 kDa 
• Atom Count: 8,441 
• Modelled Residue Count: 1,023 
• Deposited Residue Count: 1,158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome assembly protein	A, B, C, D, E, F	193	Plasmodium falciparum	Mutation(s): 0  Gene Names: B7
UniProt
Find proteins for Q9Y010 (Plasmodium falciparum) Explore Q9Y010  Go to UniProtKB:  Q9Y010

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.312 
• R-Value Work: 0.243 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.79	α = 90
b = 114.9	β = 90
c = 139.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Gill, J., Yogavel, M., Sharma, A.
• This entry supersedes: 3KYP

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references