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- PDB-6fsb: Influenza B/Memphis/13/03 endonuclease with I38T mutation -

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Basic information

Entry
Database: PDB / ID: 6fsb
TitleInfluenza B/Memphis/13/03 endonuclease with I38T mutation
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Influenza polymerase / endonuclease
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / 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
: / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
B: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1475
Polymers47,0132
Non-polymers1343
Water2,252125
1
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6163
Polymers23,5071
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5312
Polymers23,5071
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.980, 61.450, 92.630
Angle α, β, γ (deg.)90.00, 95.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23506.596 Da / Num. of mol.: 2 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Details: N-terminal GAMGSGMA linkerI38T 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 46.26 %
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

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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 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39336 / % possible obs: 91.3 % / Redundancy: 1.7 % / CC1/2: 0.996 / Rsym value: 0.055 / Net I/σ(I): 7.55
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 5269 / CC1/2: 0.596 / Rsym value: 0.58 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FML

5fml


Resolution: 1.8→46.104 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2361 1863 4.97 %
Rwork0.1968 --
obs0.1988 37473 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 3 125 3363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113397
X-RAY DIFFRACTIONf_angle_d1.0434591
X-RAY DIFFRACTIONf_dihedral_angle_d13.7592068
X-RAY DIFFRACTIONf_chiral_restr0.06500
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.3511570.32682757X-RAY DIFFRACTION97
1.8487-1.90310.31711410.32072735X-RAY DIFFRACTION94
1.9031-1.96450.34741220.29772560X-RAY DIFFRACTION90
1.9645-2.03470.34371350.27042706X-RAY DIFFRACTION95
2.0347-2.11620.31221510.25032775X-RAY DIFFRACTION95
2.1162-2.21250.2561490.22072776X-RAY DIFFRACTION98
2.2125-2.32910.25721440.20652732X-RAY DIFFRACTION95
2.3291-2.47510.26271590.20482799X-RAY DIFFRACTION97
2.4751-2.66610.21761390.19212771X-RAY DIFFRACTION96
2.6661-2.93440.27131400.18912675X-RAY DIFFRACTION92
2.9344-3.35890.23281340.17682804X-RAY DIFFRACTION97
3.3589-4.23140.19811530.15932797X-RAY DIFFRACTION95
4.2314-46.11940.18451390.18062723X-RAY DIFFRACTION92

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