+Open data
-Basic information
Entry | Database: PDB / ID: 3vnu | ||||||
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Title | Complex structure of viral RNA polymerase I | ||||||
Components |
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Keywords | TRANSLATION / TRANSFERASE/RNA / RNA POLYMERASE / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / response to antibiotic / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / response to antibiotic / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Escherichia phage Qbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Takeshita, D. / Tomita, K. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Mechanism for template-independent terminal adenylation activity of Q beta replicase Authors: Takeshita, D. / Yamashita, S. / Tomita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnu.cif.gz | 257.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnu.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnu ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnu | HTTPS FTP |
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-Related structure data
Related structure data | 3vnvC 4fwtC 3agpS 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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Unit cell |
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Components on special symmetry positions |
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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 Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Escherichia phage Qbeta (virus) Production host: Escherichia coli (E. coli) References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0 |
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-RNA chain , 2 types, 2 molecules GT
#2: RNA chain | Mass: 2421.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized RNA |
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#3: RNA chain | Mass: 2661.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized RNA |
-Non-polymers , 3 types, 15 molecules
#4: Chemical | ChemComp-ATP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30% PEG400, 0.2M calcium acetate, 0.1M HEPES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 31696 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AGP Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.839 / SU B: 32.105 / SU ML: 0.497 / Cross valid method: THROUGHOUT / σ(F): 1.48 / ESU R Free: 0.617 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.684 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.281 Å / Total num. of bins used: 20
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