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- PDB-6nem: 3-hydroxy-5-[(naphthalen-1-yl)methyl]-6-[4-(1H-tetrazol-5-yl)phen... -

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Basic information

Entry
Database: PDB / ID: 6nem
Title3-hydroxy-5-[(naphthalen-1-yl)methyl]-6-[4-(1H-tetrazol-5-yl)phenyl]pyridin-2(1H)-one bound to influenza 2009 pH1N1 endonuclease
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN/INHIBITOR / Influenza endonuclease inhibitor chelator / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
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 / Chem-KKS / : / Protein PA-X
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBauman, J.D. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119321 United States
CitationJournal: Chemmedchem / Year: 2019
Title: Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-ones: Synthesis and Evaluation as Inhibitors of Influenza A Endonuclease.
Authors: Sagong, H.Y. / Bauman, J.D. / Nogales, A. / Martinez-Sobrido, L. / Arnold, E. / LaVoie, E.J.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.title ..._citation.journal_abbrev / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry

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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)29,1626
Polymers28,5051
Non-polymers6565
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-22 kcal/mol
Surface area10750 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,32312
Polymers57,0112
Non-polymers1,31310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2370 Å2
ΔGint-56 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.505, 100.996, 66.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

MN

21A-513-

HOH

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Components

#1: Protein Polymerase acidic protein


Mass: 28505.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-KKS / 3-hydroxy-5-[(naphthalen-1-yl)methyl]-6-[4-(1H-tetrazol-5-yl)phenyl]pyridin-2(1H)-one


Mass: 395.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Crystals were formed by mixing in a 1:1 ratio the purified endonuclease protein (5 mg/ml) with crystallization buffer containing 200 mM MES pH 6.7, 27% PEG8000, 200 mM ammonium sulfate, 1 mM ...Details: Crystals were formed by mixing in a 1:1 ratio the purified endonuclease protein (5 mg/ml) with crystallization buffer containing 200 mM MES pH 6.7, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM magnesium acetate, 10 mM taurine, and 50 mM sodium fluoride. Crystals matured to full size in one to two weeks at 20 degrees C.
Temp details: 20 degree room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 41538 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.67 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.09 / Net I/σ(I): 9 / Num. measured all: 155304
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-1.983.60.79920551.0081100
1.98-2.023.60.63220951.0471100
2.02-2.063.60.53920641.0311100
2.06-2.13.60.44621001.0811100
2.1-2.153.60.35120791.0911100
2.15-2.23.70.28321161.11100
2.2-2.253.70.23920491.1021100
2.25-2.313.70.22920751.1491100
2.31-2.383.70.19720771.1461100
2.38-2.463.70.16920631.1191100
2.46-2.543.80.13520861.1411100
2.54-2.653.80.11820751.0851100
2.65-2.773.80.09821011.1131100
2.77-2.913.90.0820691.091100
2.91-3.13.90.06220551.051100
3.1-3.333.90.05321141.0561100
3.33-3.673.90.04220771.2641100
3.67-4.23.90.03720751.071100
4.2-5.293.80.03420731.074199.8
5.29-503.70.03620400.962197.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M5R

4m5r


Resolution: 1.95→40.151 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.5
RfactorNum. reflection% reflection
Rfree0.203 2091 5.04 %
Rwork0.1774 --
obs0.1787 41516 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.94 Å2 / Biso mean: 54.4845 Å2 / Biso min: 21.8 Å2
Refinement stepCycle: final / Resolution: 1.95→40.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 55 119 1820
Biso mean--44.73 52.71 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121738
X-RAY DIFFRACTIONf_angle_d1.0982342
X-RAY DIFFRACTIONf_chiral_restr0.06243
X-RAY DIFFRACTIONf_plane_restr0.007300
X-RAY DIFFRACTIONf_dihedral_angle_d12.4351038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9434-1.98860.28551340.27472465259993
1.9886-2.03830.26711390.250426602799100
2.0383-2.09340.20981440.233926362780100
2.0934-2.1550.27511380.213726432781100
2.155-2.22450.22321400.187926252765100
2.2245-2.3040.2381380.186926692807100
2.304-2.39630.20331390.18326352774100
2.3963-2.50530.21841410.171626102751100
2.5053-2.63740.17831410.168526452786100
2.6374-2.80260.20271410.172426532794100
2.8026-3.01890.21851410.16726562797100
3.0189-3.32260.19551430.186626402783100
3.3226-3.80310.17931420.163426432785100
3.8031-4.79020.16871380.148126412779100
4.7902-40.15960.22171320.18572604273698
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)
14.31181.7366-1.86373.0814-1.33472.963-0.44420.63660.0116-0.51720.14230.00480.03750.15670.2870.3416-0.1505-0.03540.35090.01370.2720.319818.3133-15.7962
23.5375-1.26520.98264.6623-1.77957.17290.3041-0.619-0.49160.4414-0.2614-0.07530.67850.0888-0.04950.3986-0.1212-0.06670.31740.07570.298810.18155.3240.751
35.47841.993-0.57497.5424-0.74115.79660.0448-0.16230.6889-0.0989-0.11340.6416-0.4864-0.58520.09470.21190.015-0.04070.2696-0.03610.32925.112720.9702-2.472
45.72962.8625-3.12513.3693-1.14626.67980.0198-0.10150.6348-0.0185-0.10350.3479-0.63390.19610.02130.3615-0.162-0.07940.261-0.03020.313317.932125.3516-1.6806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 49 )A-4 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 98 )A50 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 138 )A99 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 195 )A139 - 195

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