+Open data
-Basic information
Entry | Database: PDB / ID: 4q7j | ||||||
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Title | Complex structure of viral RNA polymerase | ||||||
Components |
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Keywords | TRANSLATION/TRANSFERASE / RNA polymerase / RNA binding motif / RNA dependent RNA polymerization / TRANSLATION-TRANSFERASE complex | ||||||
Function / homology | Function and homology information RNA secondary structure unwinding / guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / guanosine tetraphosphate binding / translational elongation / negative regulation of cytoplasmic translation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...RNA secondary structure unwinding / guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / guanosine tetraphosphate binding / translational elongation / negative regulation of cytoplasmic translation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / single-stranded RNA binding / structural constituent of ribosome / translation / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / response to antibiotic / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Enterobacteria phage Qbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Takeshita, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Molecular insights into replication initiation by Q beta replicase using ribosomal protein S1. 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 | 4q7j.cif.gz | 535.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7j.ent.gz | 434.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7j ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7j | HTTPS FTP |
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-Related structure data
Related structure data | 3agpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Elongation factor ... , 2 types, 4 molecules AEBF
#1: Protein | Mass: 30332.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsf / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P1 #2: Protein | Mass: 43209.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47 |
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-Protein , 2 types, 4 molecules CGDH
#3: Protein | Mass: 66305.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE0, UniProt: P14647*PLUS #4: Protein | Mass: 31340.545 Da / Num. of mol.: 2 / Fragment: UNP residues 1-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsA / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG67 |
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-Non-polymers , 2 types, 257 molecules
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 0.2M lithium sulfate, 20% PEG3350, pH 8.0, 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 270 / Detector: CCD / Date: Feb 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 84212 / Biso Wilson estimate: 43.49 Å2 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.58 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AGP Resolution: 2.9→19.982 Å / FOM work R set: 0.7413 / SU ML: 0.6 / σ(F): 1.51 / Phase error: 32.5 / Stereochemistry target values: ML
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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 max: 175.49 Å2 / Biso mean: 63.95 Å2 / Biso min: 6.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.982 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: 30
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