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Yorodumi- PDB-7nuh: Influenza A/California/07/2009(H1N1) endonuclease with I38T mutat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nuh | |||||||||
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Title | Influenza A/California/07/2009(H1N1) endonuclease with I38T mutation in complex with orientin | |||||||||
Components | Polymerase acidic protein,Polymerase acidic protein | |||||||||
Keywords | VIRAL PROTEIN / endonuclease / protein-ligand complex / RNA polymerase / Flavonoids | |||||||||
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 | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Radilova, K. / Brynda, J. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Synthesis and In Vitro Evaluation of C-7 and C-8 Luteolin Derivatives as Influenza Endonuclease Inhibitors. Authors: Reiberger, R. / Radilova, K. / Kral, M. / Zima, V. / Majer, P. / Brynda, J. / Dracinsky, M. / Konvalinka, J. / Kozisek, M. / Machara, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nuh.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nuh.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 7nuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nuh_validation.pdf.gz | 405.2 KB | Display | wwPDB validaton report |
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Full document | 7nuh_full_validation.pdf.gz | 406.1 KB | Display | |
Data in XML | 7nuh_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7nuh_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/7nuh ftp://data.pdbj.org/pub/pdb/validation_reports/nu/7nuh | HTTPS FTP |
-Related structure data
Related structure data | 7nugC 6ya5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21196.129 Da / Num. of mol.: 1 / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1)) Strain: A/California/07/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds |
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-Non-polymers , 6 types, 202 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-USE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 7, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→45.24 Å / Num. obs: 10985 / % possible obs: 99.2 % / Redundancy: 6.793 % / Biso Wilson estimate: 41.708 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.095 / Χ2: 0.891 / Net I/σ(I): 15.96 / Num. measured all: 74623 / Scaling rejects: 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YA5 Resolution: 2.2→45.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1533 / FOM work R set: 0.7638 / SU B: 9.178 / SU ML: 0.216 / SU R Cruickshank DPI: 0.2974 / SU Rfree: 0.2397 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.09 Å2 / Biso mean: 42.106 Å2 / Biso min: 18.17 Å2
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Refinement step | Cycle: final / Resolution: 2.2→45.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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