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Open data
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Basic information
Entry | Database: PDB / ID: 3avu | ||||||
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Title | Structure of viral RNA polymerase complex 2 | ||||||
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![]() | TRANSLATION / TRANSFERASE/RNA / RNA polymerase / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeshita, D. / Tomita, K. | ||||||
![]() | ![]() Title: Molecular basis for RNA polymerization by Q beta replicase Authors: Takeshita, D. / Tomita, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.1 KB | Display | ![]() |
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PDB format | ![]() | 199.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 543.5 KB | Display | |
Data in XML | ![]() | 49.3 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3avtC ![]() 3avvC ![]() 3avwC ![]() 3avxC ![]() 3avyC ![]() 3agpS C: citing same article ( 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 141417.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of Elongation factor Ts, Elongation factor Tu and Q beta replicase Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0 | ||
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#2: RNA chain | Mass: 2236.395 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: RNA chain | Mass: 3811.336 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Date: Jun 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 39345 / Biso Wilson estimate: 62.06 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AGP Resolution: 2.907→19.973 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.79 / SU ML: 0.38 / σ(F): 1.42 / Phase error: 28.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.14 Å2 / ksol: 0.273 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.31 Å2 / Biso mean: 82.4141 Å2 / Biso min: 24.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.907→19.973 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: 13
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