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Yorodumi- PDB-7xgc: Crystal structure of influenza polymerase acidic subunit N-termin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xgc | ||||||
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Title | Crystal structure of influenza polymerase acidic subunit N-terminal domain crystallized by ammonium sulfate with glycan | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / endo-nuclease | ||||||
Function / homology | Function and homology information cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis ...cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Viral mRNA Translation / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Guo, Y. / Hoshino, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Cryst.Growth Des. / Year: 2022 Title: Influence of Glycan Agents on Protein Crystallization with Ammonium Sulfate Authors: Guo, Y. / Hoshino, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xgc.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xgc.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xgc ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgc | HTTPS FTP |
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-Related structure data
Related structure data | 7xgqC 4zqqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22300.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PA / Plasmid: pET50b / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)pLys References: UniProt: P03433, Hydrolases; Acting on ester bonds | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.15 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1M MES, 1.275M Ammonium Sulfate, 0.1M POTASSIUM CHLORIDE, 9%(v/v) TREHALOSE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2021 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.79 Å / Num. obs: 37623 / % possible obs: 99.7 % / Redundancy: 11.8 % / Biso Wilson estimate: 29.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.174 / Num. unique obs: 1755 / CC1/2: 0.522 / Rpim(I) all: 0.495 / Rrim(I) all: 1.282 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZQQ Resolution: 1.6→37.536 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.14 Å2 / Biso mean: 34.8614 Å2 / Biso min: 19.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→37.536 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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