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- PDB-4dyb: Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-88355... -

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Basic information

Entry
Database: PDB / ID: 4dyb
TitleCrystal Structure of WSN/A Influenza Nucleoprotein with BMS-883559 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-0MH / Nucleoprotein / Nucleoprotein
Similarity search - Component
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 28, 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

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7764
Polymers113,6122
Non-polymers1,1642
Water32418
1
A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules

A: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,1646
Polymers170,4183
Non-polymers1,7463
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 area14720 Å2
ΔGint-75 kcal/mol
Surface area49110 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)172,1646
Polymers170,4183
Non-polymers1,7463
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 area9770 Å2
ΔGint-47 kcal/mol
Surface area52940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.796, 145.796, 145.796
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-0MH / N-[4-chloranyl-5-[4-[[3-(2-methoxyphenyl)-5-methyl-1,2-oxazol-4-yl]carbonyl]piperazin-1-yl]-2-nitro-phenyl]thiophene-2-carboxamide


Mass: 582.027 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24ClN5O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.27 Å3/Da / Density % sol: 45.89 %

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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→103.093 Å / Num. all: 24295 / Num. obs: 24295

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.62 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.2308 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7627 / SU B: 17.234 / SU ML: 0.346 / SU Rfree: 0.4606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 955 3.9 %RANDOM
Rwork0.2569 ---
obs0.259 24295 94.56 %-
all-24295 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.76 Å2 / Biso mean: 54.5988 Å2 / Biso min: 20.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 80 18 6220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216317
X-RAY DIFFRACTIONr_angle_refined_deg0.8821.9658577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6395840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04423.636231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72715910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2671535
X-RAY DIFFRACTIONr_chiral_restr0.0580.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024796
X-RAY DIFFRACTIONr_nbd_refined0.1760.22822
X-RAY DIFFRACTIONr_nbtor_refined0.2910.24378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.2163
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.222
X-RAY DIFFRACTIONr_mcbond_it0.34524302
X-RAY DIFFRACTIONr_mcangle_it0.6152.56623
X-RAY DIFFRACTIONr_scbond_it0.41932435
X-RAY DIFFRACTIONr_scangle_it0.7084.51954
LS refinement shellResolution: 2.8→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 70 -
Rwork0.331 1692 -
all-1762 -
obs--94.58 %

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