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Yorodumi- PDB-4or6: Structure of Influenza B PB2 cap-binding domain with Q325F mutati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4or6 | ||||||
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Title | Structure of Influenza B PB2 cap-binding domain with Q325F mutation complex with GDP | ||||||
Components | Polymerase basic protein 2 | ||||||
Keywords | VIRAL PROTEIN / cap binding | ||||||
Function / homology | : / Influenza RNA polymerase PB2 CAP binding domain / viral RNA genome replication / RNA binding / GUANOSINE-5'-DIPHOSPHATE / Polymerase basic protein 2 Function and homology information | ||||||
Biological species | influenza B virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å | ||||||
Authors | Liu, Y. / Fan, J. / Zheng, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism. Authors: Liu, Y. / Yang, Y. / Fan, J. / He, R. / Luo, M. / Zheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4or6.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4or6.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 4or6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4or6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4or6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4or6_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 4or6_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4or6 ftp://data.pdbj.org/pub/pdb/validation_reports/or/4or6 | HTTPS FTP |
-Related structure data
Related structure data | 4or4SC 4q46C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19629.664 Da / Num. of mol.: 2 / Fragment: cap-binding domain / Mutation: Q325F Source method: isolated from a genetically manipulated source Source: (gene. exp.) influenza B virus / Strain: B/Jiangxi/BV/2006 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (DE3) / References: UniProt: A0A0J9X1Y8*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. ...THIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP. RESIUDES 316-319 ARE THE EXPRESSION | |
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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: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.15M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2013 |
Radiation | Monochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. all: 17196 / Num. obs: 17179 / % possible obs: 99.9 % / Observed criterion σ(I): 3.8 / Redundancy: 9.3 % / Biso Wilson estimate: 23.52 Å2 |
Reflection shell | Resolution: 2.29→2.36 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OR4 Resolution: 2.293→30.134 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.895 / SU ML: 0.27 / σ(F): 0.72 / Phase error: 22.94 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 22.764 Å2
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Refinement step | Cycle: LAST / Resolution: 2.293→30.134 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: 6
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