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- PDB-4dyp: Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-83178... -

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Basic information

Entry
Database: PDB / ID: 4dyp
TitleCrystal Structure of WSN/A Influenza Nucleoprotein with BMS-831780 Ligand Bound
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
Chem-0MS / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5644
Polymers113,6122
Non-polymers9522
Water28816
1
A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8456
Polymers170,4183
Non-polymers1,4273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area14600 Å2
ΔGint-74 kcal/mol
Surface area49030 Å2
MethodPISA
2
B: Nucleocapsid protein
hetero molecules

B: Nucleocapsid protein
hetero molecules

B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8456
Polymers170,4183
Non-polymers1,4273
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area8900 Å2
ΔGint-61 kcal/mol
Surface area52950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.550, 146.550, 146.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Nucleocapsid protein / nucleoprotein


Mass: 56806.047 Da / Num. of mol.: 2
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: Chemical ChemComp-0MS / [4-(5-bromanyl-3-methyl-pyridin-2-yl)piperazin-1-yl]-[3-(2-chlorophenyl)-5-methyl-1,2-oxazol-4-yl]methanone


Mass: 475.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20BrClN4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.31 Å3/Da / Density % sol: 46.72 %

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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: 2.82→103.627 Å / Num. obs: 25480 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.346 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.82-2.950.6854.3735319314698.8
2.95-3.180.4487.249873451199.8
3.18-3.410.22913.3637293326599.9
3.41-3.760.12620.7740699363899.9
3.76-4.320.07231.3740699367699.9
4.32-5.480.05339.5439515362899.9
5.48-8.460.04347.0327803259399.9
8.46-10.870.03165.52565153099.6
10.87-15.860.0363.453145328100
15.860.0360.97146316595.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→48.85 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2776 / WRfactor Rwork: 0.2457 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7652 / SU B: 16.339 / SU ML: 0.324 / SU R Cruickshank DPI: 2.6956 / SU Rfree: 0.4185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.696 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 1294 5.1 %RANDOM
Rwork0.2543 ---
obs0.2564 25470 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.32 Å2 / Biso mean: 53.8592 Å2 / Biso min: 21.78 Å2
Refinement stepCycle: LAST / Resolution: 2.82→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 58 16 5935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216029
X-RAY DIFFRACTIONr_angle_refined_deg0.8611.9588213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3445837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61523.103203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8511533
X-RAY DIFFRACTIONr_chiral_restr0.0560.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024637
X-RAY DIFFRACTIONr_nbd_refined0.1760.22524
X-RAY DIFFRACTIONr_nbtor_refined0.2890.24220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.216
X-RAY DIFFRACTIONr_mcbond_it0.36324256
X-RAY DIFFRACTIONr_mcangle_it0.6552.56488
X-RAY DIFFRACTIONr_scbond_it0.48132038
X-RAY DIFFRACTIONr_scangle_it0.7794.51725
LS refinement shellResolution: 2.82→2.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 89 -
Rwork0.349 1758 -
all-1847 -
obs--99.68 %

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