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- PDB-5x7v: Crystal structure of Nucleosome assembly protein S (PfNapS) from ... -

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Basic information

Entry
Database: PDB / ID: 5x7v
TitleCrystal structure of Nucleosome assembly protein S (PfNapS) from Plasmodium falciparum
ComponentsNucleosome assembly protein
KeywordsCHAPERONE / NUCLEOSOME ASSEMBLY PROTEIN / HISTONE RECOGNITION
Function / homology
Function and homology information


protein tetramerization / nucleosome assembly / nucleus
Similarity search - Function
Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / p53-like tetramerisation domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleosome assembly protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.802 Å
AuthorsGill, J. / Yogavel, M. / Sharma, A.
CitationJournal: Malar. J. / Year: 2010
Title: Structure, localization and histone binding properties of nuclear-associated nucleosome assembly protein from Plasmodium falciparum.
Authors: Gill, J. / Kumar, A. / Yogavel, M. / Belrhali, H. / Jain, S.K. / Rug, M. / Brown, M. / Maier, A.G. / Sharma, A.
History
DepositionFeb 27, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 15, 2017ID: 3KYP
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleosome assembly protein
B: Nucleosome assembly protein
C: Nucleosome assembly protein
D: Nucleosome assembly protein
E: Nucleosome assembly protein
F: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)137,9596
Polymers137,9596
Non-polymers00
Water00
1
A: Nucleosome assembly protein
B: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)45,9862
Polymers45,9862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-36 kcal/mol
Surface area18930 Å2
MethodPISA
2
C: Nucleosome assembly protein
D: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)45,9862
Polymers45,9862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-33 kcal/mol
Surface area19410 Å2
MethodPISA
3
E: Nucleosome assembly protein
F: Nucleosome assembly protein


Theoretical massNumber of molelcules
Total (without water)45,9862
Polymers45,9862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-34 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.790, 114.900, 139.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleosome assembly protein


Mass: 22993.096 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 29-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: B7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y010

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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: 2.77 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 3350, 0.2M di-ammonuium tatrate, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35024 / % possible obs: 96.6 % / Redundancy: 5.9 % / Net I/σ(I): 23.5
Reflection shellResolution: 2.8→2.9 Å / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.802→29.244 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 44.2
RfactorNum. reflection% reflection
Rfree0.3119 1697 4.96 %
Rwork0.2433 --
obs0.2467 34206 89.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→29.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8441 0 0 0 8441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128832
X-RAY DIFFRACTIONf_angle_d1.45211893
X-RAY DIFFRACTIONf_dihedral_angle_d17.6263377
X-RAY DIFFRACTIONf_chiral_restr0.0581263
X-RAY DIFFRACTIONf_plane_restr0.0071509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8021-2.88450.4529890.36791872X-RAY DIFFRACTION62
2.8845-2.97750.49711090.33962117X-RAY DIFFRACTION71
2.9775-3.08380.33171220.30452307X-RAY DIFFRACTION77
3.0838-3.20720.38561370.30712542X-RAY DIFFRACTION85
3.2072-3.35290.35771450.29842753X-RAY DIFFRACTION92
3.3529-3.52940.29731510.26042856X-RAY DIFFRACTION95
3.5294-3.75010.34111530.22982893X-RAY DIFFRACTION96
3.7501-4.0390.30381480.22712930X-RAY DIFFRACTION97
4.039-4.44420.27051550.2082972X-RAY DIFFRACTION98
4.4442-5.08430.26121600.19663010X-RAY DIFFRACTION99
5.0843-6.39470.27971610.24783076X-RAY DIFFRACTION99
6.3947-29.24520.30261670.21823181X-RAY DIFFRACTION99

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