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- PDB-4dyt: Crystal Structure of WSN/A Influenza Nucleoprotein with Three Mut... -

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Basic information

Entry
Database: PDB / ID: 4dyt
TitleCrystal Structure of WSN/A Influenza Nucleoprotein with Three Mutations (E53D, Y289H, Y313V)
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 / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)170,5023
Polymers170,5023
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-61 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.460, 135.930, 191.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nucleocapsid protein / nucleoprotein


Mass: 56834.148 Da / Num. of mol.: 3 / Mutation: E53D,Y289H,Y313V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/WSN/1933(H1N1) / Gene: NP / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: B4URF1, UniProt: Q1K9H2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.29 Å3/Da / Density % sol: 46.4 %

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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: 3→45.08 Å / Num. all: 28852 / Num. obs: 28852

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.08 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.337 / WRfactor Rwork: 0.2728 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7214 / SU B: 30.175 / SU ML: 0.56 / SU Rfree: 0.5909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.591 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3416 945 3.3 %RANDOM
Rwork0.2699 ---
obs0.2723 28850 91.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.24 Å2 / Biso mean: 82.4367 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 3→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 0 13 8534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0218658
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.9311784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6651279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70923.322298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94615951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3291557
X-RAY DIFFRACTIONr_chiral_restr0.0570.21311
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026873
X-RAY DIFFRACTIONr_nbd_refined0.2010.23893
X-RAY DIFFRACTIONr_nbtor_refined0.2910.25968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0420.24
X-RAY DIFFRACTIONr_mcbond_it0.37826465
X-RAY DIFFRACTIONr_mcangle_it0.6892.59733
X-RAY DIFFRACTIONr_scbond_it0.44532476
X-RAY DIFFRACTIONr_scangle_it0.7434.52051
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 66 -
Rwork0.402 2022 -
all-2088 -
obs--95.43 %

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