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Yorodumi- PDB-5if7: Crystal structure of polymerase acid protein (PA) from Influenza ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5if7 | ||||||
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Title | Crystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to fragment hit EBSI-279 N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / NIAID / structural genomics / flu / fragment screening / STD NMR / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To Be Published Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5if7.cif.gz | 175.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5if7.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 5if7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5if7_validation.pdf.gz | 690.6 KB | Display | wwPDB validaton report |
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Full document | 5if7_full_validation.pdf.gz | 694.9 KB | Display | |
Data in XML | 5if7_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5if7_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/5if7 ftp://data.pdbj.org/pub/pdb/validation_reports/if/5if7 | HTTPS FTP |
-Related structure data
Related structure data | 5ieqC 5if2C 5if5C 5if8C 5ifbC 5ifcC 5ifdC 4iujS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53096.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1) Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659 |
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#2: Chemical | ChemComp-6AY / |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mg/mL protein against Morpheus screen condition H6 10% PEG 8000, 20% EG, 0.02 M each amino acid, 0.1 M MOPS/Hepes pH 7.5, unique puck ID pyl5-5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→44.546 Å / Num. obs: 15474 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IUJ Resolution: 2.65→44.546 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.93 Å2 / Biso mean: 52.8644 Å2 / Biso min: 22.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→44.546 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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