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- PDB-5n2u: Influenza D virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 5n2u
TitleInfluenza D virus nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / influenza virus / nucleoprotein
Function / homologyInfluenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / host cell nucleus / structural molecule activity / RNA binding / NP
Function and homology information
Biological speciesInfluenza D virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLabaronne, A. / Ruigrok, R.W.H. / Crepin, T.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0017 France
French National Research AgencyANR-10-LABX-49-01 France
CitationJournal: Sci Rep / Year: 2019
Title: The structure of the nucleoprotein of Influenza D shows that all Orthomyxoviridae nucleoproteins have a similar NPCORE, with or without a NPTAILfor nuclear transport.
Authors: Donchet, A. / Oliva, J. / Labaronne, A. / Tengo, L. / Miloudi, M. / C A Gerard, F. / Mas, C. / Schoehn, G. / W H Ruigrok, R. / Ducatez, M. / Crepin, T.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)245,5614
Polymers245,5614
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17480 Å2
ΔGint-84 kcal/mol
Surface area76810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.166, 85.166, 103.385
Angle α, β, γ (deg.)91.20, 101.94, 101.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoprotein


Mass: 61390.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus (D/bovine/France/2986/2012)
Gene: NP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3VZU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.35→44.44 Å / Num. obs: 93538 / % possible obs: 91.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 51.41 Å2 / CC1/2: 0.994 / Rsym value: 0.093 / Net I/σ(I): 7.78
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 8505 / CC1/2: 0.366 / Rsym value: 0.847 / % possible all: 94.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDP

3zdp


Resolution: 2.4→39.71 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.87 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.245 / SU Rfree Cruickshank DPI: 0.256
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4331 4.93 %RANDOM
Rwork0.202 ---
obs0.205 87872 91.4 %-
Displacement parametersBiso mean: 55.71 Å2
Baniso -1Baniso -2Baniso -3
1--7.1107 Å214.0055 Å212.8684 Å2
2--4.8748 Å2-9.0738 Å2
3---2.2359 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.4→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14646 0 0 235 14881
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1519978HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5401SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes388HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2116HARMONIC5
X-RAY DIFFRACTIONt_it14886HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion20.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1947SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17337SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 334 4.95 %
Rwork0.219 6418 -
all0.22 6752 -
obs--94.39 %

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