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- PDB-7kbc: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7kbc
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / cleaved / DNA BINDING PROTEIN
Function / homology
Function and homology information


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
Baloxavir acid / : / Hexa Vinylpyrrolidone K15 / Protein PA-X / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCuypers, M.G. / Kumar, G. / Slavish, J. / White, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Authors: Kumar, G. / Cuypers, M. / Webby, R.R. / Webb, T.R. / White, S.W.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Downloads & links

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Assembly

Deposited unit
A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,95311
Polymers23,1341
Non-polymers1,81910
Water88349
1
A: Protein PA-X
hetero molecules

A: Protein PA-X
hetero molecules

A: Protein PA-X
hetero molecules

A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,81244
Polymers92,5374
Non-polymers7,27540
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11120 Å2
ΔGint-126 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.963, 89.963, 133.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23134.316 Da / Num. of mol.: 1 / Mutation: E119D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA-X / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4P2TE19, UniProt: C6H0Y9, UniProt: A0A5J6VBC3*PLUS

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Non-polymers , 6 types, 59 molecules

#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.93 Å3/Da / Density % sol: 58 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→44.98 Å / Num. obs: 12694 / % possible obs: 94.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 768 / CC1/2: 0.692 / Rpim(I) all: 0.377 / % possible all: 65.3

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.25→44.98 Å / SU ML: 0.3147 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 679 5.35 %
Rwork0.195 12008 -
obs0.1969 12687 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.79 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 111 49 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611600
X-RAY DIFFRACTIONf_angle_d1.16192156
X-RAY DIFFRACTIONf_chiral_restr0.0655221
X-RAY DIFFRACTIONf_plane_restr0.0073268
X-RAY DIFFRACTIONf_dihedral_angle_d18.9914586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.430.3396920.2821880X-RAY DIFFRACTION75.73
2.43-2.670.29381360.25782438X-RAY DIFFRACTION98.09
2.67-3.060.26951540.22752494X-RAY DIFFRACTION99.96
3.06-3.850.20941370.18782545X-RAY DIFFRACTION100
3.85-44.980.2051600.17012651X-RAY DIFFRACTION99.96
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)
15.73620391623-2.725571064763.456324333854.986538515852.016465816887.37763177373-0.2581060398710.270987146071-0.975003048423-1.949981588430.4666604440691.278360059980.006747469829780.824078390774-0.4074641709520.7568351889060.03208539699690.05601685648340.708821186670.1136053185690.47984856066821.1804418704-16.42438617013.60454101115
29.081628516242.843548160030.8706936487445.94628090432.253629764936.98690054398-0.363277309291.472014438530.951561097004-1.185691428820.219470049485-0.415346524644-1.22938990760.8306752952110.1770665244750.778499016716-0.04110669009070.03824060706250.8042748763840.2618713180180.51692098539126.766072337-5.358414189164.42032816435
32.109839893950.302994300233-1.563402690446.201862764891.198816372153.42225179719-0.2324659766060.2178824646330.174508520479-0.1670924558140.05331061573620.530789950574-0.2062771002720.2364407434510.1725146523110.3487936779930.079857582191-0.06119981847650.5053214550020.1572087277880.33891110066319.4070782119-3.7322892414816.8792489712
47.702611042423.31823762716-5.100876527413.61613265929-2.647459883386.28709268755-0.945590292291-0.3187985869420.8280624544130.0400488439979-0.470069180473-0.106712013284-0.8632171366931.405240591690.121359721680.4832339674-0.106982705722-0.2051340212520.816605127010.1309357200250.39737783917526.132028960111.153725128318.8605479923
53.02540142099-0.618635224431-0.4010636065995.274056157931.391104617451.29810951328-0.329246659021-0.3053811147420.0264207987181.268459363230.382150427542-0.7628118109780.5095119303950.588385264074-0.04372747223160.5159114724110.133029660165-0.1825710899320.7441815547870.08248659510080.404411044325.8485523261-0.26355111791125.2735025955
65.59501112214-0.328217711356-0.6613551896193.247697786130.5574736736019.08947403439-0.354884573064-0.5632900110650.3148348304030.6730836896740.182784840461-1.180802596711.14813684758-0.168397005257-0.1092613709760.6826914521230.310817751111-0.2541993930581.141947764580.06103428983150.69697764758134.0957543568-9.4933607303827.5370342822
72.80520205805-0.02456728640210.3981842896627.095446529491.455387115477.84192273675-0.17696755092-0.3349908017090.06141478358130.919529608655-0.124788882038-0.1850497716550.3354755636580.1920709452630.2664645146410.5497120166110.197848471188-0.06989071000530.7017808992020.1635018740090.37409294905323.9357880546-8.3985747342329.555774266
83.62976247518-1.28841563462-2.475266627738.081769394164.446345967263.69656157809-0.07877268125550.248697863513-0.3334350830310.518988160648-0.241275165990.51564136920.776826150457-0.337118224210.1132881015660.5276264532410.1400953136320.02162267253110.4679136705710.1803796393630.4311674716116.9320362071-18.551140529918.9553095382
95.113653792563.65873199942-3.084521822578.908803033934.643221034169.503755494720.158315147048-0.387714137119-0.759244141958-0.604158703628-0.504491187442-0.6711284066310.9115920751010.7703410021930.3007057300180.6330311152790.327447328964-0.001968843763550.9932376345270.06771358821620.5416180235529.9204536913-22.242811223813.0440118917
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 -2 through 10 )-2 - 102 - 14
22chain 'A' and (resid 11 through 31 )11 - 3115 - 35
33chain 'A' and (resid 32 through 83 )32 - 8336 - 68
44chain 'A' and (resid 84 through 98 )84 - 9869 - 83
55chain 'A' and (resid 99 through 126 )99 - 12684 - 111
66chain 'A' and (resid 127 through 138 )127 - 138112 - 123
77chain 'A' and (resid 139 through 164 )139 - 164124 - 149
88chain 'A' and (resid 165 through 185 )165 - 185150 - 170
99chain 'A' and (resid 186 through 195 )186 - 195171 - 180

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