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Open data
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Basic information
Entry | Database: PDB / ID: 3avw | ||||||
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Title | Structure of viral RNA polymerase complex 4 | ||||||
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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 | ![]() | 262.6 KB | Display | ![]() |
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PDB format | ![]() | 203.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 819.9 KB | Display | ![]() |
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Full document | ![]() | 871.4 KB | Display | |
Data in XML | ![]() | 48.7 KB | Display | |
Data in CIF | ![]() | 67.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3avtC ![]() 3avuC ![]() 3avvC ![]() 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
-Protein , 1 types, 1 molecules A
#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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-RNA chain , 2 types, 2 molecules GT
#2: RNA chain | Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: RNA chain | Mass: 3811.336 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 107 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GH3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GH3.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-GH3 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.19 % |
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-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: 2.6→50 Å / Num. obs: 55827 / Biso Wilson estimate: 44.34 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AGP Resolution: 2.602→19.987 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8304 / SU ML: 0.36 / σ(F): 1.46 / Phase error: 24.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.7 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.17 Å2 / Biso mean: 55.5328 Å2 / Biso min: 13.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.602→19.987 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: 19
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