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Open data
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Basic information
Entry | Database: PDB / ID: 5wop | ||||||
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Title | High Resolution Structure of Mutant CA09-PB2cap | ||||||
![]() | Polymerase PB2 | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / viral RNA genome replication / ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Constantinides, A.E. / Gumpper, R.H. / Severin, C. / Luo, M. | ||||||
![]() | ![]() Title: High-resolution structure of the Influenza A virus PB2cap binding domain illuminates the changes induced by ligand binding. Authors: Constantinides, A. / Gumpper, R. / Severin, C. / Luo, M. #1: ![]() Title: The cap-binding site of influenza virus protein PB2 as a drug target Authors: Severin, C. / Rocha de Moura, T. / Liu, Y. / Li, K. / Zheng, X. / Luo, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.2 KB | Display | ![]() |
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PDB format | ![]() | 220 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eg7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17837.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % / Description: Prism |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.86 Details: 0.1 M ammonium acetate, 0.1 M Bis Tris, pH 5.86, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2017 | |||||||||||||||||||||
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection | Resolution: 1.52→72.43 Å / Num. obs: 47950 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Net I/σ(I): 11 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5EG7 Resolution: 1.52→39 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.059 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.43 Å2 / Biso mean: 21.183 Å2 / Biso min: 2.33 Å2
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Refinement step | Cycle: final / Resolution: 1.52→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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