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- PDB-8vgz: Influenza PA-N Endonuclease E23K Mutant (amino acids 52-74 truncation) -

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Basic information

Entry
Database: PDB / ID: 8vgz
TitleInfluenza PA-N Endonuclease E23K Mutant (amino acids 52-74 truncation)
ComponentsProtein PA-X
KeywordsHYDROLASE / Influenza endonuclease / resistance / drug discovery / metal-binding pharmacophore
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / viral RNA genome replication / RNA binding / metal ion binding / : / Protein PA-X
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKohlbrand, A.J. / 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: Biochemistry / Year: 2024
Title: Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants.
Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M.
History
DepositionDec 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8723
Polymers20,7621
Non-polymers1102
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.152, 75.152, 120.134
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-411-

HOH

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Components

#1: Protein Protein PA-X


Mass: 20761.744 Da / Num. of mol.: 1 / Mutation: E23K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: PA-X / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5J6VBC3
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% 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: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→65.08 Å / Num. obs: 19860 / % possible obs: 99 % / Redundancy: 18.5 % / Biso Wilson estimate: 47.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.2
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 1198 / CC1/2: 0.173

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→65.08 Å / SU ML: 0.6149 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.0523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2752 1991 10.03 %
Rwork0.218 17869 -
obs0.2237 19860 88.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.91 Å2
Refinement stepCycle: LAST / Resolution: 2.09→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 2 18 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451487
X-RAY DIFFRACTIONf_angle_d0.66871996
X-RAY DIFFRACTIONf_chiral_restr0.0447213
X-RAY DIFFRACTIONf_plane_restr0.0053255
X-RAY DIFFRACTIONf_dihedral_angle_d4.3575196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.3498370.4566382X-RAY DIFFRACTION26.17
2.14-2.20.44231410.42491206X-RAY DIFFRACTION85.09
2.2-2.270.45581170.45881001X-RAY DIFFRACTION69.31
2.27-2.340.4186870.4074869X-RAY DIFFRACTION59.71
2.34-2.420.41091570.3831446X-RAY DIFFRACTION98.77
2.42-2.520.41621530.36471425X-RAY DIFFRACTION99.81
2.52-2.640.3471550.30741450X-RAY DIFFRACTION99.88
2.64-2.770.35431630.28271437X-RAY DIFFRACTION100
2.77-2.950.33921650.26211437X-RAY DIFFRACTION99.94
2.95-3.180.33891640.26231446X-RAY DIFFRACTION100
3.18-3.490.27151650.19661429X-RAY DIFFRACTION100
3.5-40.261610.1771449X-RAY DIFFRACTION99.94
4-5.040.18881580.14911448X-RAY DIFFRACTION99.94
5.04-65.080.23411680.16991444X-RAY DIFFRACTION100
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)
18.029600369422.53021921838-0.4437212017743.490897415380.4149205886474.414353638990.1597446175631.02301616949-0.539686567738-0.09695606918790.15787239021-0.1472669701120.172655174390.0427604775872-0.4224218108230.6142956101190.0583719546760.08067948979340.501973651645-0.1199221256880.43191770873729.5037.142-20.435
26.78900398073-0.55628190456-0.0494320396212.926026264810.1188744528011.771297514880.0309919260078-0.329813565004-0.4270137886320.021600512333-0.02881923603520.509570238150.0771318793801-0.2415769029870.02474975722260.4172624608290.001007027765730.05866840543620.3070079575210.01398161882970.43096461162415.03512.863-8.667
35.28169955882-0.589010786726-1.436087877242.57934133229-0.9128029902283.95312295360.320209275262-0.1523085322710.3458999942780.106898320359-0.09748321013410.32688577607-0.420628206390.0391402669641-0.2205656999190.508739941647-0.04348865333430.007192481848560.235404256049-0.02758721853580.32688976534827.26719.371-5.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:31 )A-1 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 32:126 )A32 - 126
3X-RAY DIFFRACTION3( CHAIN A AND RESID 127:195 )A127 - 195

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