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- PDB-6fs9: Influenza B/Memphis/13/03 endonuclease with I38T mutation with bo... -

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Basic information

Entry
Database: PDB / ID: 6fs9
TitleInfluenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Influenza polymerase / endonuclease / inhibitor
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
Baloxavir acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsCusack, S. / Speranzini, V.
CitationJournal: Sci Rep / Year: 2018
Title: Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil.
Authors: Omoto, S. / Speranzini, V. / Hashimoto, T. / Noshi, T. / Yamaguchi, H. / Kawai, M. / Kawaguchi, K. / Uehara, T. / Shishido, T. / Naito, A. / Cusack, S.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1716
Polymers23,5071
Non-polymers6645
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-20 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.710, 63.710, 125.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 23506.596 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Details: N-terminal GAMGSGMA linker, I38T mutation / Source: (gene. exp.) Influenza B virus (B/Memphis/13/2003) / Gene: PA / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for ...Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.28→56.8 Å / Num. obs: 10663 / % possible obs: 93.5 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rsym value: 0.044 / Net I/σ(I): 16.1
Reflection shellResolution: 2.28→2.34 Å / Mean I/σ(I) obs: 2.37 / CC1/2: 0.899 / Rsym value: 0.561

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:5FML

5fml


Resolution: 2.28→56.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.359 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 516 4.8 %RANDOM
Rwork0.17911 ---
obs0.18177 10147 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.623 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å2-0 Å2-0 Å2
2--2.55 Å2-0 Å2
3----5.1 Å2
Refinement stepCycle: 1 / Resolution: 2.28→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 38 8 1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021549
X-RAY DIFFRACTIONr_bond_other_d0.0020.021417
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9942094
X-RAY DIFFRACTIONr_angle_other_deg1.06433299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61725.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69515285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.89157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4646.038726
X-RAY DIFFRACTIONr_mcbond_other5.4496.038725
X-RAY DIFFRACTIONr_mcangle_it7.3429.038904
X-RAY DIFFRACTIONr_mcangle_other7.3439.039905
X-RAY DIFFRACTIONr_scbond_it6.5996.614823
X-RAY DIFFRACTIONr_scbond_other6.5956.612824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.539.6571191
X-RAY DIFFRACTIONr_long_range_B_refined11.29967.2781716
X-RAY DIFFRACTIONr_long_range_B_other11.29767.281717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.279→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 35 -
Rwork0.272 794 -
obs--99.76 %

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