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- PDB-8dde: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 8dde
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-2-(1H-tetrazol-5-yl) yridine-3-ol
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / HYDROLASE-INHIBITOR complex
Function / homology: / Chem-R7C
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors.
Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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)22,7924
Polymers22,4241
Non-polymers3683
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.979, 75.979, 121.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-317-

HOH

31A-348-

HOH

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Components

#1: Protein Polymerase acidic protein / Protein PA-X


Mass: 22424.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-R7C / (2M)-6-bromo-3-hydroxy-2-(1H-tetrazol-5-yl)pyridin-4(1H)-one


Mass: 258.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4BrN5O2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→65.83 Å / Num. obs: 19284 / % possible obs: 100 % / Redundancy: 26.2 % / Biso Wilson estimate: 53.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.017 / Rrim(I) all: 0.085 / Net I/σ(I): 25
Reflection shellResolution: 2.22→2.3 Å / Rmerge(I) obs: 1.183 / Num. unique obs: 1055 / CC1/2: 0.883 / Rpim(I) all: 0.237 / Rrim(I) all: 1.207

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.22→57.81 Å / SU ML: 0.3398 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 1938 10.05 %
Rwork0.1875 17346 -
obs0.1932 19284 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.51 Å2
Refinement stepCycle: LAST / Resolution: 2.22→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 16 52 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00981505
X-RAY DIFFRACTIONf_angle_d1.03162025
X-RAY DIFFRACTIONf_chiral_restr0.0555217
X-RAY DIFFRACTIONf_plane_restr0.0079258
X-RAY DIFFRACTIONf_dihedral_angle_d19.3542557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.44131380.34651214X-RAY DIFFRACTION97.55
2.28-2.340.30291400.26971229X-RAY DIFFRACTION99.64
2.34-2.410.36251380.24611219X-RAY DIFFRACTION99.85
2.41-2.480.3571390.25171268X-RAY DIFFRACTION100
2.48-2.570.35971390.23691226X-RAY DIFFRACTION99.78
2.57-2.680.33541440.23981241X-RAY DIFFRACTION99.86
2.68-2.80.33261420.22571252X-RAY DIFFRACTION99.93
2.8-2.940.29711360.23651227X-RAY DIFFRACTION99.93
2.94-3.130.27121350.20811245X-RAY DIFFRACTION100
3.13-3.370.24791390.20581239X-RAY DIFFRACTION100
3.37-3.710.28071340.17031245X-RAY DIFFRACTION100
3.71-4.250.16021410.15781250X-RAY DIFFRACTION100
4.25-5.350.17761360.14441240X-RAY DIFFRACTION99.93
5.35-57.810.24491370.17781251X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.715366490495.85048012438-0.3276259972927.55389478644-2.027313487458.90985707645-0.312665979570.987435742495-0.420957555263-0.5364013403870.5264352906280.3766042252110.28533656653-0.165260732514-0.1238647212350.6562582528810.07199146354480.04868893871520.496933371117-0.1097875681790.57952345645329.22493279897.54645638632-20.131684177
26.87167987212-0.00180966260082-1.271068208040.8205717253210.04677297555431.778745149590.167739392234-0.026313348694-0.04892891424460.0639905853324-0.08470528106940.358595143212-0.137426036354-0.100027302917-0.09723721007730.599746661527-0.01769073017790.07984781707980.331391616904-0.01017518162460.49494240595615.368676481812.9627593266-8.178116507
38.50795504483-1.49753687012-0.2189015612876.9549731649-1.421001686723.35035673991-0.0171402667411-0.4916889061390.769608813940.4873455804710.07570649108760.210790270351-0.593980124589-0.0677730848149-0.06835353619560.607814203829-0.03000006424140.07824274314740.353610924674-0.06702640631530.48370967671421.091458751823.6165406451-3.16009316083
45.827315872382.79742214302-0.03003865576427.86413753865-1.947903543856.724925706310.3617713467460.2087317862970.23865453961-0.17603036838-0.142117687446-0.0163309798011-0.3064939558320.117268038416-0.1133622555270.4457026442530.08078343918480.009358849216840.2880540520710.005008344708310.31985763110435.393776990315.5774635674-7.82412571832
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )1 - 313 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 108
33chain 'A' and (resid 127 through 164 )127 - 164109 - 146
44chain 'A' and (resid 165 through 197 )165 - 197147 - 179

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