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- PDB-4or6: Structure of Influenza B PB2 cap-binding domain with Q325F mutati... -
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Open data
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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 | ||||||
![]() | Polymerase basic protein 2 | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Fan, J. / Zheng, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.7 KB | Display | ![]() |
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PDB format | ![]() | 62.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4or4SC ![]() 4q46C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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