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- PDB-6vll: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6vll
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease mutant I38T in complex with SJ000986213
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
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-R3J / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
Citation
Journal: To Be Published
Title: The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000986213
Authors: Cuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
#1: Journal: 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
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)23,8245
Polymers23,1361
Non-polymers6874
Water41423
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)190,59040
Polymers185,0908
Non-polymers5,50032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area20290 Å2
ΔGint-207 kcal/mol
Surface area59510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.693, 90.693, 132.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Polymerase acidic protein


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
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 BL21(DE3) (bacteria) / References: UniProt: C6H0Y9
#2: Chemical ChemComp-R3J / benzyl [2-(5-hydroxy-4-{[2-(2-methoxypyridin-4-yl)ethyl]carbamoyl}-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate


Mass: 481.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N5O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 2.94 Å3/Da / Density % sol: 58.21 %
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: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→74.83 Å / Num. obs: 6270 / % possible obs: 95.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Χ2: 0.7 / Net I/σ(I): 13.4
Reflection shellResolution: 2.87→3.03 Å / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 903 / Rpim(I) all: 0.349 / Rrim(I) all: 1.007 / Χ2: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.87→64.21 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 0.008 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.437
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 467 7.5 %RANDOM
Rwork0.2352 ---
obs0.2387 5769 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.13 Å2 / Biso mean: 80.461 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å2-0 Å20 Å2
2--3.61 Å2-0 Å2
3----7.22 Å2
Refinement stepCycle: final / Resolution: 2.87→64.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 32 23 1504
Biso mean--99.12 59.75 -
Num. residues----182
LS refinement shellResolution: 2.87→2.945 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 37 -
Rwork0.323 412 -
all-449 -
obs--96.56 %

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