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- PDB-4w9s: 2-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxypyrimidin-4(3H)-one bound... -

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Basic information

Entry
Database: PDB / ID: 4w9s
Title2-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxypyrimidin-4(3H)-one bound to influenza 2009 H1N1 endonuclease
ComponentsPolymerase acidic protein
Keywordstranscription/transcription inhibitor / CAP-SNATCHING / RNA BINDING PROTEIN / RNA BINDING PROTEIN-INHIBITOR COMPLEX / transcription-transcription inhibitor complex
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 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
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
Similarity search - Domain/homology
Chem-3K1 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBauman, J.D. / Patel, D. / Das, K. / Arnold, E.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Phenyl Substituted 4-Hydroxypyridazin-3(2H)-ones and 5-Hydroxypyrimidin-4(3H)-ones: Inhibitors of Influenza A Endonuclease.
Authors: Sagong, H.Y. / Bauman, J.D. / Patel, D. / Das, K. / Arnold, E. / LaVoie, E.J.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_refine_tls_group.selection_details / _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 / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_keywords.text

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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)29,0636
Polymers28,5051
Non-polymers5585
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.986, 101.637, 66.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 28505.270 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Hokkaido/8/1980 H3N8 / Gene: PA / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P13166
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-3K1 / 5-hydroxy-2-[4-(1H-tetrazol-5-yl)phenyl]pyrimidin-4(3H)-one


Mass: 256.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Crystals are formed by mixing in a 1:1 ratio endonuclease (5 mg/ml) with crystallization buffer containing 200 mM MES, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM ...Details: Crystals are formed by mixing in a 1:1 ratio endonuclease (5 mg/ml) with crystallization buffer containing 200 mM MES, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM magnesium acetate, 10 mM taurine, and 50 mM sodium fluoride. Crystals form within a few hours and grow to maximum size in one to two weeks

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: . X-ray diffraction data collection was performed at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline. The diffraction data were indexed, processed, scaled and ...Ambient temp details: . X-ray diffraction data collection was performed at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline. The diffraction data were indexed, processed, scaled and merged using HKL2000.29 The structure was solved and refined using the software PHENIX.30
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.8→22.9 Å / Num. all: 27807 / Num. obs: 27807 / % possible obs: 99.31 % / Redundancy: 3.5 % / Net I/σ(I): 22.39
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.83 / % possible all: 99.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M5Q

4m5q


Resolution: 1.8→22.9 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1395 5 %Random 5%
Rwork0.1756 ---
obs0.1773 27807 99.31 %-
Refinement stepCycle: LAST / Resolution: 1.8→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 31 153 1830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121710
X-RAY DIFFRACTIONf_angle_d1.282301
X-RAY DIFFRACTIONf_dihedral_angle_d15.134641
X-RAY DIFFRACTIONf_chiral_restr0.053241
X-RAY DIFFRACTIONf_plane_restr0.007295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.86420.33031010.30392626X-RAY DIFFRACTION98
1.8642-1.93880.33351430.27082607X-RAY DIFFRACTION100
1.9388-2.02690.2841540.22732603X-RAY DIFFRACTION100
2.0269-2.13370.20471460.20132620X-RAY DIFFRACTION100
2.1337-2.26730.23371380.17312634X-RAY DIFFRACTION100
2.2673-2.44220.24141300.18642660X-RAY DIFFRACTION100
2.4422-2.68760.20561520.17412659X-RAY DIFFRACTION100
2.6876-3.07570.17271390.1772655X-RAY DIFFRACTION100
3.0757-3.8720.2151530.15982668X-RAY DIFFRACTION100
3.872-22.91570.17991390.1542680X-RAY DIFFRACTION95
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)
14.63191.8488-0.69253.918-1.79083.6361-0.42080.8143-0.1974-0.37580.2633-0.08850.1730.27290.08170.4776-0.14730.02240.496-0.01670.288621.4518.635-18.593
24.24022.3893-0.66377.5416-4.9767.3079-0.1141-0.3525-0.51220.2922-0.1635-0.35760.08290.13890.35970.3147-0.061-0.00980.25860.03290.298516.42612.714-0.832
32.660.34280.40452.13-0.8684.43810.1946-0.2973-0.11610.2436-0.30390.10560.3938-0.52940.04740.3269-0.1106-0.00610.2822-0.01750.29767.00711.042-2.324
44.82210.7678-0.67418.3593-3.00922.91980.16650.30381.3906-0.02270.0081.1422-0.8044-0.7375-0.2390.45390.0684-0.02340.4918-0.07060.6064.99926.44-1.207
54.61341.888-1.7581.67510.00834.37950.0086-0.19760.5686-0.1298-0.15920.1952-0.73790.5008-0.0790.475-0.1572-0.05650.3245-0.01190.37320.72526.033-2.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -4:31 )A-4 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 32:62 )A32 - 62
3X-RAY DIFFRACTION3( CHAIN A AND RESID 63:126 )A63 - 126
4X-RAY DIFFRACTION4( CHAIN A AND RESID 127:149 )A127 - 149
5X-RAY DIFFRACTION5( CHAIN A AND RESID 150:195 )A150 - 195

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