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- PDB-6v9e: The crystal structure of the 2009 H1N1 PA endonuclease wild type ... -

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Basic information

Entry
Database: PDB / ID: 6v9e
TitleThe crystal structure of the 2009 H1N1 PA endonuclease wild type in complex with SJ000988632
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / HYDROLASE
Function / homology
Function and homology information


viral translational frameshifting / viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
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
: / Chem-QQP / Chem-Y24 / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,3726
Polymers23,1481
Non-polymers1,2245
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.052, 91.052, 134.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polymerase acidic protein


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-QQP / N-[2-(6-amino-9H-purin-9-yl)ethyl]-5-hydroxy-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide


Mass: 460.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15F3N8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-Y24 / 1,1',1'',1''',1''''-[(3R,5S,7S,9R)-decane-1,3,5,7,9-pentayl]penta(pyrrolidin-2-one)


Mass: 557.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H47N5O5
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→64.38 Å / Num. obs: 11142 / % possible obs: 98.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 72.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.017 / Rrim(I) all: 0.038 / Χ2: 1.1 / Net I/σ(I): 20.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1145 / CC1/2: 0.812 / Rpim(I) all: 0.403 / Rrim(I) all: 0.908 / Χ2: 1.04 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17rc1_3605refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.4→38.96 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.84
RfactorNum. reflection% reflection
Rfree0.2748 582 5.23 %
Rwork0.2439 --
obs0.2454 11131 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.96 Å2 / Biso mean: 83.2572 Å2 / Biso min: 41.66 Å2
Refinement stepCycle: final / Resolution: 2.4→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 80 45 1545
Biso mean--111.03 83.59 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.640.42411570.37382586274399
2.64-3.020.41591330.35652607274098
3.02-3.810.35311450.29542678282399
3.81-38.960.21481470.19552678282595

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