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- PDB-5ega: 2009 H1N1 PA endonuclease domain in complex with an N-acylhydrazo... -

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Basic information

Entry
Database: PDB / ID: 5ega
Title2009 H1N1 PA endonuclease domain in complex with an N-acylhydrazone inhibitor
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / influenza / endonuclease / HYDROLASE-HYDROLASE INHIBITOR complex
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 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
Chem-GK0 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: Sci Rep / Year: 2016
Title: N-acylhydrazone inhibitors of influenza virus PA endonuclease with versatile metal binding modes.
Authors: Carcelli, M. / Rogolino, D. / Gatti, A. / De Luca, L. / Sechi, M. / Kumar, G. / White, S.W. / Stevaert, A. / Naesens, L.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)22,4004
Polymers21,9701
Non-polymers4303
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.989, 73.989, 128.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Polymerase acidic protein


Mass: 21970.160 Da / Num. of mol.: 1
Fragment: endonuclease domain (UNP residues 1-50, 73-196 connected by GGS linker)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Plasmid: pET52b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GK0 / 3,4,5-tris(oxidanyl)-~{N}-[(~{E})-[3,4,5-tris(oxidanyl)phenyl]methylideneamino]benzamide


Mass: 320.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97121 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 14, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 11896 / % possible obs: 99.4 % / Redundancy: 16.7 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.018 / Rrim(I) all: 0.073 / Χ2: 1.192 / Net I/av σ(I): 42.847 / Net I/σ(I): 11.8 / Num. measured all: 198693
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.23150.9311560.8630.2410.9620.77899.7
2.23-2.32170.68211570.9450.1670.7030.80799.9
2.32-2.4217.40.4911510.9660.1180.5040.87100
2.42-2.5517.40.31111710.9860.0750.321.004100
2.55-2.7117.30.21411680.990.0520.221.234100
2.71-2.9217.30.15111830.9940.0370.1551.392100
2.92-3.2117.20.11612000.9970.0280.121.468100
3.21-3.68170.07611910.9980.0180.0781.356100
3.68-4.6316.70.0612340.9990.0150.0621.44899.5
4.63-5014.90.0412850.9990.010.0411.48895.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data scaling
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DES

5des


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 10.822 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 627 5.3 %RANDOM
Rwork0.2055 ---
obs0.2071 11252 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: 128.72 Å2 / Biso mean: 62.204 Å2 / Biso min: 38.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.22 Å20 Å2
2---0.43 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 25 32 1462
Biso mean--87.32 62.76 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191459
X-RAY DIFFRACTIONr_bond_other_d0.0020.021315
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9531971
X-RAY DIFFRACTIONr_angle_other_deg0.96633004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46822.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83615242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8831513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it2.2894.703707
X-RAY DIFFRACTIONr_mcbond_other2.2894.699706
X-RAY DIFFRACTIONr_mcangle_it3.4357.038882
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 42 -
Rwork0.199 801 -
all-843 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: -21.6126 Å / Origin y: 13.6994 Å / Origin z: -7.6328 Å
111213212223313233
T0.0651 Å2-0.0265 Å20.0358 Å2-0.0765 Å20.0695 Å2--0.1712 Å2
L1.6031 °20.0416 °2-0.4662 °2-1.6789 °2-0.4993 °2--2.0369 °2
S0.0212 Å °-0.0001 Å °0.2568 Å °-0.0936 Å °-0.1544 Å °-0.2485 Å °-0.0748 Å °0.1381 Å °0.1332 Å °

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