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

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Basic information

Entry
Database: PDB / ID: 8dal
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 4-(benzyloxy)-6-bromo-3-hydroxypicolinonitrile
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / HYDROLASE-INHIBITOR complex
Function / homology: / Chem-R6O
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7494
Polymers22,4251
Non-polymers3253
Water1,74797
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)75.403, 75.403, 120.436
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-334-

HOH

21A-339-

HOH

31A-389-

HOH

41A-391-

HOH

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Components

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


Mass: 22424.547 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-R6O / 6-bromo-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carbonitrile


Mass: 215.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3BrN2O2 / 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.: 97 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Description: Hexagonal shaped crystals typically 50 to 150 microns in size.
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→40.15 Å / Num. obs: 19468 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 45.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Rrim(I) all: 0.092 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 1.368 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1049 / CC1/2: 0.589 / Rpim(I) all: 0.415 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
APEX 2data reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.2→40.15 Å / SU ML: 0.3255 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 1960 10.07 %
Rwork0.1998 17508 -
obs0.2055 19468 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 13 97 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391502
X-RAY DIFFRACTIONf_angle_d0.56762018
X-RAY DIFFRACTIONf_chiral_restr0.0416216
X-RAY DIFFRACTIONf_plane_restr0.004256
X-RAY DIFFRACTIONf_dihedral_angle_d4.6109199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.38661420.30861240X-RAY DIFFRACTION99.64
2.25-2.320.30441400.30191265X-RAY DIFFRACTION100
2.32-2.380.31491380.27591251X-RAY DIFFRACTION100
2.38-2.460.31621380.25961240X-RAY DIFFRACTION100
2.46-2.550.29911370.25861239X-RAY DIFFRACTION99.78
2.55-2.650.34451440.26221262X-RAY DIFFRACTION99.93
2.65-2.770.38381460.25891262X-RAY DIFFRACTION100
2.77-2.920.31931410.25351237X-RAY DIFFRACTION100
2.92-3.10.28541310.23281248X-RAY DIFFRACTION99.86
3.1-3.340.2621350.22561257X-RAY DIFFRACTION100
3.34-3.680.21711350.17191251X-RAY DIFFRACTION100
3.68-4.210.2381440.15771261X-RAY DIFFRACTION99.93
4.21-5.30.19241440.14331238X-RAY DIFFRACTION100
5.3-40.150.23821450.18531257X-RAY DIFFRACTION99.79
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)
13.711201023864.7935979743-1.451252786416.41031389108-2.738482644663.89440297984-0.0156884213340.934227202633-0.436046888244-0.7046993909570.2870355641620.5001229105340.56467736313-0.183808436877-0.2417376743440.5806429552530.02866662604430.01711937903990.508287181751-0.1231393375090.54296299596229.29535597357.53966239395-20.3377308602
27.690670038070.495106056562-1.811337482071.20472377601-0.6820824138631.822336061940.0509150850287-0.20942833739-0.1464632393240.156520565741-0.08403570911160.2676198796250.0542729695259-0.222628520190.05677832677960.419210060505-0.01705059155320.05532589264810.293967464502-0.01297509937820.3371292339215.14914062912.9421070999-8.44951811988
37.85582789929-1.36563429111-0.6858095469831.64278823252-0.1784500811282.402127655860.213720272634-0.09851698385910.3088092683190.0657887533778-0.1621365845140.0586181224633-0.126722322277-0.0549246670503-0.07856665652210.444159208149-0.03396367409060.005498971269440.233737656597-0.04288466092370.32531255943427.577749230819.689511124-5.65149305837
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 - 311 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 107
33chain 'A' and (resid 127 through 198 )127 - 198108 - 179

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