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- PDB-5dbs: 2009 H1N1 PA endonuclease mutant E119D in complex with dTMP -

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Basic information

Entry
Database: PDB / ID: 5dbs
Title2009 H1N1 PA endonuclease mutant E119D in complex with dTMP
ComponentsPolymerase acidic protein
KeywordsHYDROLASE / influenza / resistance / endonuclease inhibitor / viral protein
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THYMIDINE-5'-PHOSPHATE / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI098757 United States
St. Jude Children's Research Hospital (ALSAC) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor.
Authors: Song, M.S. / Kumar, G. / Shadrick, W.R. / Zhou, W. / Jeevan, T. / Li, Z. / Slavish, P.J. / Fabrizio, T.P. / Yoon, S.W. / Webb, T.R. / Webby, R.J. / White, S.W.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6084
Polymers23,1341
Non-polymers4733
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,43016
Polymers92,5374
Non-polymers1,89312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_885-x+3,-y+3,z1
crystal symmetry operation3_855-y+3,x,z1
crystal symmetry operation4_585y,-x+3,z1
Buried area8220 Å2
ΔGint-131 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.390, 90.390, 133.293
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: 23134.316 Da / Num. of mol.: 1 / Mutation: E119D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3W5S0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 58.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 4, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16301 / % possible obs: 99.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Χ2: 1.186 / Net I/av σ(I): 28.954 / Net I/σ(I): 12.3 / Num. measured all: 200012
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.106-2.186.40.72815580.9070.2750.7810.77798.2
2.18-2.268.20.68716050.9580.2360.7280.82699.9
2.26-2.3710.50.67216160.9820.2090.7050.856100
2.37-2.4912.90.65916150.9860.1890.6860.905100
2.49-2.6514.20.48416030.9910.1330.5020.994100
2.65-2.8514.40.31616190.990.0870.3281.152100
2.85-3.1414.40.17616250.9950.0480.1821.32499.9
3.14-3.5914.30.11216440.9960.0310.1171.489100
3.59-4.5214.20.08716620.9970.0240.0911.51999.9
4.52-5012.90.06617540.9980.0190.0691.46799

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZN

5czn


Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.017 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 867 5.3 %RANDOM
Rwork0.2085 ---
obs0.2102 15432 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.98 Å2 / Biso mean: 62.66 Å2 / Biso min: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 27 16 1456
Biso mean--69.88 58.49 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191470
X-RAY DIFFRACTIONr_bond_other_d0.0020.021319
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9511988
X-RAY DIFFRACTIONr_angle_other_deg0.99533022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17322.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_mcbond_it1.9963.777715
X-RAY DIFFRACTIONr_mcbond_other1.9973.776714
X-RAY DIFFRACTIONr_mcangle_it3.1955.655892
LS refinement shellResolution: 2.106→2.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 62 -
Rwork0.274 1085 -
all-1147 -
obs--96.14 %
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)
13.4028-0.20091.08450.121-0.1831.34780.0147-0.2159-0.02190.0119-0.1412-0.0170.5128-0.11270.12650.4363-0.12950.15890.26610.00730.0853128.2073111.5355417.8859
215.37512.5748-9.827437.438414.239624.5593-0.48630.46770.20820.47940.19590.67541.039-0.45150.29040.1384-0.03970.00950.03650.04310.1515126.6208105.1095415.8108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 176
2X-RAY DIFFRACTION2E1

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