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- PDB-4dys: Crystal Structure of Apo Swine Flu Influenza Nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4dys
TitleCrystal Structure of Apo Swine Flu Influenza Nucleoprotein
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R.
CitationJournal: To be Published
Title: To be determined
Authors: Lewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)157,4643
Polymers157,4643
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-62 kcal/mol
Surface area53370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.345, 94.345, 603.804
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Nucleocapsid protein / nucleoprotein


Mass: 52487.910 Da / Num. of mol.: 3 / Fragment: UNP residues 26-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NP / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: G8XKZ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.46 Å3/Da / Density % sol: 50.06 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→100.504 Å / Num. all: 40964 / Num. obs: 40256 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.375 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.990.7412.0218937440096.4
2.99-3.230.4433.2817306407395.7
3.23-3.560.2086.7318100407996.5
3.56-4.090.09813.5717656403795.1
4.09-4.980.05523.515584344993.1
4.98-6.320.04725.949449215591.7
6.32-8.110.02939.545068110590.3
8.11-11.840.01960.31290667289.2
11.84-18.940.01661.07109724385.9
18.940.01761.633468278.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→51.85 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.821 / WRfactor Rfree: 0.2828 / WRfactor Rwork: 0.2246 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8206 / SU B: 16.824 / SU ML: 0.334 / SU Rfree: 0.4272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 1619 4 %RANDOM
Rwork0.241 ---
obs0.2431 38632 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.6 Å2 / Biso mean: 38.1425 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→51.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9867 0 0 39 9906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02110026
X-RAY DIFFRACTIONr_angle_refined_deg0.821.94513543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.20251334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83822.715383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.392151609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3271585
X-RAY DIFFRACTIONr_chiral_restr0.0530.21523
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027531
X-RAY DIFFRACTIONr_nbd_refined0.1660.24497
X-RAY DIFFRACTIONr_nbtor_refined0.290.27001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.29
X-RAY DIFFRACTIONr_mcbond_it0.3426799
X-RAY DIFFRACTIONr_mcangle_it0.6072.510487
X-RAY DIFFRACTIONr_scbond_it0.3633670
X-RAY DIFFRACTIONr_scangle_it0.6114.53056
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 118 -
Rwork0.315 2633 -
all-2751 -
obs--93.29 %

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